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Metabolomics: Official Journal of the Metabolomic Society

Cong-Hui Yao, Gao-Yuan Liu, Kui Yang, Richard W Gross, Gary J Patti
INTRODUCTION: Palmitate, the typical end product released from fatty acid synthase, is of interest to many researchers performing metabolomics. Although palmitate can be readily detected by using mass spectrometry, many metabolomic platforms involve the use of plastic consumables that introduce a competing background signal of palmitate. OBJECTIVES: The goal of this study was to quantify palmitate contamination in metabolomics and isotope tracer studies and to examine the reliability of approaches for reducing error...
September 2016: Metabolomics: Official Journal of the Metabolomic Society
Drew Neavin, Rima Kaddurah-Daouk, Richard Weinshilboum
INTRODUCTION: The initial decades of the 21(st) century have witnessed striking technical advances that have made it possible to detect, identify and quantitatively measure large numbers of plasma or tissue metabolites. In parallel, similar advances have taken place in our ability to sequence DNA and RNA. Those advances have moved us beyond studies of single metabolites and single genetic polymorphisms to the study of hundreds or thousands of metabolites and millions of genomic variants in a single cell or subject...
July 2016: Metabolomics: Official Journal of the Metabolomic Society
Andrew N Lane, Richard M Higashi, Teresa W-M Fan
AIMS: In this review we compare the advantages and disadvantages of different model biological systems for determining the metabolic functions of cells in complex environments, how they may change in different disease states, and respond to therapeutic interventions. BACKGROUND: All preclinical drug-testing models have advantages and drawbacks. We compare and contrast established cell, organoid and animal models with ex vivo organ or tissue culture and in vivo human experiments in the context of metabolic readout of drug efficacy...
July 2016: Metabolomics: Official Journal of the Metabolomic Society
Shradha Wali, Rishein Gupta, Jieh-Juen Yu, Adelphe Mfuh, Xiaoli Gao, M Neal Guentzel, James P Chambers, Sazaly Abu Bakar, Guangming Zhong, Bernard P Arulanandam
INTRODUCTION: Chlamydia trachomatis (Ct), is the leading cause of sexually transmitted infections worldwide. Host transcriptomic- or proteomic profiling studies have identified key molecules involved in establishment of Ct infection or the generation of anti Ct-immunity. However, the contribution of the host metabolome is not known. OBJECTIVES: The objective of this study was to determine the contribution of host metabolites in genital Ct infection. METHODS: We used high-performance liquid chromatography-mass spectrometry, and mapped lipid profiles in genital swabs obtained from female guinea pigs at days 3, 9, 15, 30 and 65 post Ct serovar D intravaginal infection...
April 2016: Metabolomics: Official Journal of the Metabolomic Society
Lara R Dugas, Elin Chorell, Jacob Plange-Rhule, Estelle V Lambert, Guichan Cao, Richard S Cooper, Brian T Layden, Denise Scholten, Tommy Olsson, Amy Luke, Julia H Goedecke
In developed countries, specific metabolites have been associated with obesity and metabolic diseases, e.g. type 2 diabetes. It is unknown whether a similar profile persists across populations of African-origin, at increased risk for obesity and related diseases. In a cross-sectional study of normal-weight and obese black women (33.3 ± 6.3 years) from the US (N = 69, 65 % obese), South Africa (SA, N = 97, 49 % obese) and Ghana (N = 82, 33 % obese) serum metabolite profiles were characterized via gas chromatography-time of flight/mass spectrometry...
March 2016: Metabolomics: Official Journal of the Metabolomic Society
Andreea Geamanu, Smiti V Gupta, Christian Bauerfeld, Lobelia Samavati
Sarcoidosis is a systemic granulomatous disease of unknown etiology. Granulomatous inflammation in sarcoidosis may affect multiple organs, including the lungs, skin, CNS, and the eyes, leading to severe morbidity and mortality. The underlying mechanisms for sustained inflammation in sarcoidosis are unknown. We hypothesized that metabolic changes play a critical role in perpetuation of inflammation in sarcoidosis. (1)H nuclear magnetic resonance (NMR)-based untargeted metabolomic analysis was used to identify circulating molecules in serum to discriminate sarcoidosis patients from healthy controls...
February 2016: Metabolomics: Official Journal of the Metabolomic Society
Carl Brunius, Lin Shi, Rikard Landberg
INTRODUCTION: Liquid chromatography-mass spectrometry (LC-MS) is a commonly used technique in untargeted metabolomics owing to broad coverage of metabolites, high sensitivity and simple sample preparation. However, data generated from multiple batches are affected by measurement errors inherent to alterations in signal intensity, drift in mass accuracy and retention times between samples both within and between batches. These measurement errors reduce repeatability and reproducibility and may thus decrease the power to detect biological responses and obscure interpretation...
2016: Metabolomics: Official Journal of the Metabolomic Society
Tony Karlsborn, A K M Firoj Mahmud, Hasan Tükenmez, Anders S Byström
INTRODUCTION: The Elongator complex, comprising six subunits (Elp1p-Elp6p), is required for formation of 5-carbamoylmethyl (ncm(5)) and 5-methoxycarbonylmethyl (mcm(5)) side chains on wobble uridines in 11 out of 42 tRNA species in Saccharomyces cerevisiae. Loss of these side chains reduces the efficiency of tRNA decoding during translation, resulting in pleiotropic phenotypes. Overexpression of hypomodified [Formula: see text], which in wild-type strains are modified with mcm(5)s(2)U, partially suppress phenotypes of an elp3Δ strain...
2016: Metabolomics: Official Journal of the Metabolomic Society
Dorothea Lesche, Roland Geyer, Daniel Lienhard, Christos T Nakas, Gaëlle Diserens, Peter Vermathen, Alexander B Leichtle
BACKGROUND: Centrifugation is an indispensable procedure for plasma sample preparation, but applied conditions can vary between labs. AIM: Determine whether routinely used plasma centrifugation protocols (1500×g 10 min; 3000×g 5 min) influence non-targeted metabolomic analyses. METHODS: Nuclear magnetic resonance spectroscopy (NMR) and High Resolution Mass Spectrometry (HRMS) data were evaluated with sparse partial least squares discriminant analyses and compared with cell count measurements...
2016: Metabolomics: Official Journal of the Metabolomic Society
Olivier Fernandez, Maria Urrutia, Stéphane Bernillon, Catherine Giauffret, François Tardieu, Jacques Le Gouis, Nicolas Langlade, Alain Charcosset, Annick Moing, Yves Gibon
BACKGROUND: In the last decade, metabolomics has emerged as a powerful diagnostic and predictive tool in many branches of science. Researchers in microbes, animal, food, medical and plant science have generated a large number of targeted or non-targeted metabolic profiles by using a vast array of analytical methods (GC-MS, LC-MS, (1)H-NMR….). Comprehensive analysis of such profiles using adapted statistical methods and modeling has opened up the possibility of using single or combinations of metabolites as markers...
2016: Metabolomics: Official Journal of the Metabolomic Society
Caroline Ivanne Le Roy, Luke John Mappley, Roberto Marcello La Ragione, Martin John Woodward, Sandrine Paule Claus
INTRODUCTION: Poultry is one of the most consumed meat in the world and its related industry is always looking for ways to improve animal welfare and productivity. It is therefore essential to understand the metabolic response of the chicken to new feed formulas, various supplements, infections and treatments. OBJECTIVES: As a basis for future research investigating the impact of diet and infections on chicken's metabolism, we established a high-resolution proton nuclear magnetic resonance (NMR)-based metabolic atlas of the healthy chicken (Gallus gallus)...
2016: Metabolomics: Official Journal of the Metabolomic Society
Stéphane Grison, Gaëlle Favé, Matthieu Maillot, Line Manens, Olivia Delissen, Éric Blanchardon, Isabelle Dublineau, Jocelyne Aigueperse, Sandra Bohand, Jean-Charles Martin, Maâmar Souidi
INTRODUCTION: Data are sparse about the potential health risks of chronic low-dose contamination of humans by uranium (natural or anthropogenic) in drinking water. Previous studies report some molecular imbalances but no clinical signs due to uranium intake. OBJECTIVES: In a proof-of-principle study, we reported that metabolomics is an appropriate method for addressing this chronic low-dose exposure in a rat model (uranium dose: 40 mg L(-1); duration: 9 months, n = 10)...
2016: Metabolomics: Official Journal of the Metabolomic Society
Gregory D Tredwell, Jacob G Bundy, Maria De Iorio, Timothy M D Ebbels
INTRODUCTION: Despite the use of buffering agents the (1)H NMR spectra of biofluid samples in metabolic profiling investigations typically suffer from extensive peak frequency shifting between spectra. These chemical shift changes are mainly due to differences in pH and divalent metal ion concentrations between the samples. This frequency shifting results in a correspondence problem: it can be hard to register the same peak as belonging to the same molecule across multiple samples. The problem is especially acute for urine, which can have a wide range of ionic concentrations between different samples...
2016: Metabolomics: Official Journal of the Metabolomic Society
Caroline Muschet, Gabriele Möller, Cornelia Prehn, Martin Hrabě de Angelis, Jerzy Adamski, Janina Tokarz
INTRODUCTION: Although cultured cells are nowadays regularly analyzed by metabolomics technologies, some issues in study setup and data processing are still not resolved to complete satisfaction: a suitable harvesting method for adherent cells, a fast and robust method for data normalization, and the proof that metabolite levels can be normalized to cell number. OBJECTIVES: We intended to develop a fast method for normalization of cell culture metabolomics samples, to analyze how metabolite levels correlate with cell numbers, and to elucidate the impact of the kind of harvesting on measured metabolite profiles...
2016: Metabolomics: Official Journal of the Metabolomic Society
Douglas B Kell, Stephen G Oliver
BACKGROUND: The term 'metabolome' was introduced to the scientific literature in September 1998. AIM AND KEY SCIENTIFIC CONCEPTS OF THE REVIEW: To mark its 18-year-old 'coming of age', two of the co-authors of that paper review the genesis of metabolomics, whence it has come and where it may be going.
2016: Metabolomics: Official Journal of the Metabolomic Society
Richard D Beger, Warwick Dunn, Michael A Schmidt, Steven S Gross, Jennifer A Kirwan, Marta Cascante, Lorraine Brennan, David S Wishart, Matej Oresic, Thomas Hankemeier, David I Broadhurst, Andrew N Lane, Karsten Suhre, Gabi Kastenmüller, Susan J Sumner, Ines Thiele, Oliver Fiehn, Rima Kaddurah-Daouk
INTRODUCTION BACKGROUND TO METABOLOMICS: Metabolomics is the comprehensive study of the metabolome, the repertoire of biochemicals (or small molecules) present in cells, tissues, and body fluids. The study of metabolism at the global or "-omics" level is a rapidly growing field that has the potential to have a profound impact upon medical practice. At the center of metabolomics, is the concept that a person's metabolic state provides a close representation of that individual's overall health status...
2016: Metabolomics: Official Journal of the Metabolomic Society
Emily G Armitage, Andrew D Southam
INTRODUCTION: Cellular metabolism is altered during cancer initiation and progression, which allows cancer cells to increase anabolic synthesis, avoid apoptosis and adapt to low nutrient and oxygen availability. The metabolic nature of cancer enables patient cancer status to be monitored by metabolomics and lipidomics. Additionally, monitoring metabolic status of patients or biological models can be used to greater understand the action of anticancer therapeutics. OBJECTIVES: Discuss how metabolomics and lipidomics can be used to (i) identify metabolic biomarkers of cancer and (ii) understand the mechanism-of-action of anticancer therapies...
2016: Metabolomics: Official Journal of the Metabolomic Society
Elisabete Carvalho, Pietro Franceschi, Antje Feller, Lorena Herrera, Luisa Palmieri, Panagiotis Arapitsas, Samantha Riccadonna, Stefan Martens
INTRODUCTION: Raspberries are becoming increasingly popular due to their reported health beneficial properties. Despite the presence of only trace amounts of anthocyanins, yellow varieties seems to show similar or better effects in comparison to conventional raspberries. OBJECTIVES: The aim of this work is to characterize the metabolic differences between red and yellow berries, focussing on the compounds showing a higher concentration in yellow varieties. METHODS: The metabolomic profile of 13 red and 12 yellow raspberries (of different varieties, locations and collection dates) was determined by UPLC-TOF-MS...
2016: Metabolomics: Official Journal of the Metabolomic Society
Anastasios Mastrokolias, Rene Pool, Eleni Mina, Kristina M Hettne, Erik van Duijn, Roos C van der Mast, GertJan van Ommen, Peter A C 't Hoen, Cornelia Prehn, Jerzy Adamski, Willeke van Roon-Mom
INTRODUCTION: Metabolic changes have been frequently associated with Huntington's disease (HD). At the same time peripheral blood represents a minimally invasive sampling avenue with little distress to Huntington's disease patients especially when brain or other tissue samples are difficult to collect. OBJECTIVES: We investigated the levels of 163 metabolites in HD patient and control serum samples in order to identify disease related changes. Additionally, we integrated the metabolomics data with our previously published next generation sequencing-based gene expression data from the same patients in order to interconnect the metabolomics changes with transcriptional alterations...
2016: Metabolomics: Official Journal of the Metabolomic Society
Giuseppe Martano, Luca Murru, Edoardo Moretto, Laura Gerosa, Giulia Garrone, Vittorio Krogh, Maria Passafaro
INTRODUCTION: Neurons have a very high energy requirement, and their metabolism is tightly regulated to ensure delivery of adequate substrate to sustain neuronal activity and neuroplastic changes. The mechanisms underlying the regulation of neuronal metabolism, however, are not completely clear. OBJECTIVE: The objective of this study was to investigate the central carbon metabolism in neurons, in order to identify the regulatory pathways governing neuronal anabolism and catabolism...
2016: Metabolomics: Official Journal of the Metabolomic Society
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