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Metabolomics: Official Journal of the Metabolomic Society

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https://www.readbyqxmd.com/read/28090199/mastr-ms-a-web-based-collaborative-laboratory-information-management-system-lims-for-metabolomics
#1
Adam Hunter, Saravanan Dayalan, David De Souza, Brad Power, Rodney Lorrimar, Tamas Szabo, Thu Nguyen, Sean O'Callaghan, Jeremy Hack, James Pyke, Amsha Nahid, Roberto Barrero, Ute Roessner, Vladimir Likic, Dedreia Tull, Antony Bacic, Malcolm McConville, Matthew Bellgard
BACKGROUND: An increasing number of research laboratories and core analytical facilities around the world are developing high throughput metabolomic analytical and data processing pipelines that are capable of handling hundreds to thousands of individual samples per year, often over multiple projects, collaborations and sample types. At present, there are no Laboratory Information Management Systems (LIMS) that are specifically tailored for metabolomics laboratories that are capable of tracking samples and associated metadata from the beginning to the end of an experiment, including data processing and archiving, and which are also suitable for use in large institutional core facilities or multi-laboratory consortia as well as single laboratory environments...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28090198/computational-tools-and-workflows-in-metabolomics-an-international-survey-highlights-the-opportunity-for-harmonisation-through-galaxy
#2
Ralf J M Weber, Thomas N Lawson, Reza M Salek, Timothy M D Ebbels, Robert C Glen, Royston Goodacre, Julian L Griffin, Kenneth Haug, Albert Koulman, Pablo Moreno, Markus Ralser, Christoph Steinbeck, Warwick B Dunn, Mark R Viant
No abstract text is available yet for this article.
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/28058041/integration-of-pharmacometabolomics-with-pharmacokinetics-and-pharmacodynamics-towards-personalized-drug-therapy
#3
Vasudev Kantae, Elke H J Krekels, Michiel J Van Esdonk, Peter Lindenburg, Amy C Harms, Catherijne A J Knibbe, Piet H Van der Graaf, Thomas Hankemeier
Personalized medicine, in modern drug therapy, aims at a tailored drug treatment accounting for inter-individual variations in drug pharmacology to treat individuals effectively and safely. The inter-individual variability in drug response upon drug administration is caused by the interplay between drug pharmacology and the patients' (patho)physiological status. Individual variations in (patho)physiological status may result from genetic polymorphisms, environmental factors (including current/past treatments), demographic characteristics, and disease related factors...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27980503/stability-of-targeted-metabolite-profiles-of-urine-samples-under-different-storage-conditions
#4
Markus Rotter, Stefan Brandmaier, Cornelia Prehn, Jonathan Adam, Sylvia Rabstein, Katarzyna Gawrych, Thomas Brüning, Thomas Illig, Heiko Lickert, Jerzy Adamski, Rui Wang-Sattler
INTRODUCTION: Few studies have investigated the influence of storage conditions on urine samples and none of them used targeted mass spectrometry (MS). OBJECTIVES: We investigated the stability of metabolite profiles in urine samples under different storage conditions using targeted metabolomics. METHODS: Pooled, fasting urine samples were collected and stored at -80 °C (biobank standard), -20 °C (freezer), 4 °C (fridge), ~9 °C (cool pack), and ~20 °C (room temperature) for 0, 2, 8 and 24 h...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27980502/granulocyte-colony-stimulating-factor-alters-the-systemic-metabolomic-profile-in-healthy-donors
#5
Kimberley Joanne Hatfield, Guro Kristin Melve, Øystein Bruserud
INTRODUCTION: Peripheral blood stem cells mobilized by granulocyte colony-stimulating factor (G-CSF) from healthy donors are commonly used for allogeneic stem cell transplantation. The effect of G-CSF administration on global serum metabolite profiles has not been investigated before. OBJECTIVES: This study aims to examine the systemic metabolomic profiles prior to and following administration of G-CSF in healthy adults. METHODS: Blood samples were collected from 15 healthy stem cell donors prior to and after administration of G-CSF 10 µg/kg/day for 4 days...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27980501/the-degradation-of-nucleotide-triphosphates-extracted-under-boiling-ethanol-conditions-is-prevented-by-the-yeast-cellular-matrix
#6
Andres Gil, David Siegel, Silke Bonsing-Vedelaar, Hjalmar Permentier, Dirk-Jan Reijngoud, Frank Dekker, Rainer Bischoff
INTRODUCTION: Boiling ethanol extraction is a frequently used method for metabolomics studies of biological samples. However, the stability of several central carbon metabolites, including nucleotide triphosphates, and the influence of the cellular matrix on their degradation have not been addressed. OBJECTIVES: To study how a complex cellular matrix extracted from yeast (Saccharomyces cerevisiae) may affect the degradation profiles of nucleotide triphosphates extracted under boiling ethanol conditions...
2017: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27721678/inaccurate-quantitation-of-palmitate-in-metabolomics-and-isotope-tracer-studies-due-to-plastics
#7
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
https://www.readbyqxmd.com/read/27872580/untargeted-polar-metabolomics-of-transformed-mda-mb-231-breast-cancer-cells-expressing-varying-levels-of-human-arylamine-n-acetyltransferase-1
#8
Samantha M Carlisle, Patrick J Trainor, Xinmin Yin, Mark A Doll, Marcus W Stepp, J Christopher States, Xiang Zhang, David W Hein
INTRODUCTION: Human arylamine N-acetyltransferase 1 (NAT1) is a phase II xenobiotic metabolizing enzyme found in almost all tissues. Expression of NAT1 is elevated in several cancers including breast cancer. However, the exact mechanism by which NAT1 expression affects cancer risk and progression remains unclear. OBJECTIVE: This study explored polar metabolome differences between MDA-MB-231 breast cancer cells expressing varying levels of NAT1 activity using an untargeted approach...
July 2016: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27516730/pharmacometabolomics-informs-pharmacogenomics
#9
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
https://www.readbyqxmd.com/read/27489532/preclinical-models-for-interrogating-drug-action-in-human-cancers-using-stable-isotope-resolved-metabolomics-sirm
#10
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
https://www.readbyqxmd.com/read/27642272/guinea-pig-genital-tract-lipidome-reveals-in-vivo-and-in-vitro-regulation-of-phosphatidylcholine-16-0-18-1-and-contribution-to-chlamydia-trachomatis-serovar-d-infectivity
#11
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
https://www.readbyqxmd.com/read/27346989/obesity-related-metabolite-profiles-of-black-women-spanning-the-epidemiologic-transition
#12
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
https://www.readbyqxmd.com/read/27489531/metabolomics-connects-aberrant-bioenergetic-transmethylation-and-gut-microbiota-in-sarcoidosis
#13
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
https://www.readbyqxmd.com/read/28003796/a-novel-targeted-untargeted-gc-orbitrap-metabolomics-methodology-applied-to-candida-albicans-and-staphylococcus-aureus-biofilms
#14
Stefan Weidt, Jennifer Haggarty, Ryan Kean, Cristian I Cojocariu, Paul J Silcock, Ranjith Rajendran, Gordon Ramage, Karl E V Burgess
INTRODUCTION: Combined infections from Candida albicans and Staphylococcus aureus are a leading cause of death in the developed world. Evidence suggests that Candida enhances the virulence of Staphylococcus-hyphae penetrate through tissue barriers, while S. aureus tightly associates with the hyphae to obtain entry to the host organism. Indeed, in a biofilm state, C. albicans enhances the antimicrobial resistance characteristics of S. aureus. The association of these microorganisms is also associated with significantly increased morbidity and mortality...
2016: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27840599/circulating-sterols-as-predictors-of-early-allograft-dysfunction-and-clinical-outcome-in-patients-undergoing-liver-transplantation
#15
Uta Ceglarek, Kathleen Kresse, Susen Becker, Georg Martin Fiedler, Joachim Thiery, Markus Quante, Robert Wieland, Michael Bartels, Gabriela Aust
INTRODUCTION: Sensitive and specific assessment of the hepatic graft metabolism after liver transplantation (LTX) is essential for early detection of postoperative dysfunction implying the need for consecutive therapeutic interventions. OBJECTIVES: Here, we assessed circulating liver metabolites of the cholesterol pathway, amino acids and acylcarnitines and evaluated their predictive value on early allograft dysfunction (EAD) and clinical outcome in the context of LTX...
2016: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27840598/plasma-metabolomic-profiles-in-association-with-type-2-diabetes-risk-and-prevalence-in-chinese-adults
#16
Danxia Yu, Steven C Moore, Charles E Matthews, Yong-Bing Xiang, Xianglan Zhang, Yu-Tang Gao, Wei Zheng, Xiao-Ou Shu
Metabolomic studies have identified several metabolites associated with type 2 diabetes (T2D) in populations of European ancestry. East Asians, a population of particular susceptibility to T2D, were generally not included in previous studies. We examined the associations of plasma metabolites with risk and prevalence of T2D in 976 Chinese men and women (40-74 years of age) who were participants of two prospective cohort studies and had no cardiovascular disease or cancer at baseline. Sixty-eight prevalent and 73 incident T2D cases were included...
January 2016: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27829829/the-pretransplant-systemic-metabolic-profile-reflects-a-risk-of-acute-graft-versus-host-disease-after-allogeneic-stem-cell-transplantation
#17
Håkon Reikvam, Kimberley Hatfield, Øystein Bruserud
Allogeneic stem cell transplantation is used in the treatment of younger patients with severe hematological diseases, especially hematological malignancies, and acute graft versus host disease (GVHD) is then an important immune-mediated posttransplant complication. Several risk factors for acute GVHD have been identified, including pretransplant factors that possibly influence the posttranspant course through their effects on host immunocompetent cells. Metabolic regulation is important for immunoregulation, and we therefore investigated whether the pretransplant metabolic status of allotransplant recipients was associated with later acute GVHD...
2016: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/27746707/large-scale-untargeted-lc-ms-metabolomics-data-correction-using-between-batch-feature-alignment-and-cluster-based-within-batch-signal-intensity-drift-correction
#18
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
https://www.readbyqxmd.com/read/27738410/loss-of-ncm-5-and-mcm-5-wobble-uridine-side-chains-results-in-an-altered-metabolic-profile
#19
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
https://www.readbyqxmd.com/read/27729833/does-centrifugation-matter-centrifugal-force-and-spinning-time-alter-the-plasma-metabolome
#20
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
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