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"Untargeted metabolomics"

Yue Song, Tingting Chai, Zhiqiang Yin, Xining Zhang, Wei Zhang, Yongzhong Qian, Jing Qiu
Ibuprofen (IBU), as a commonly used non-steroidal anti-inflammatory drug (NSAID) and pharmaceutical and personal care product (PPCP), is frequently prescribed by doctors to relieve pain. It is widely released into environmental water and soil in the form of chiral enantiomers by the urination and defecation of humans or animals and by sewage discharge from wastewater treatment plants. This study focused on the alteration of metabolism in the adult zebrafish (Danio rerio) brain after exposure to R-(-)-/S-(+)-/rac-IBU at 5 μg L-1 for 28 days...
June 9, 2018: Environmental Pollution
Zhucui Li, Yan Lu, Yufeng Guo, Haijie Cao, Qinhong Wang, Wenqing Shui
Data analysis represents a key challenge for untargeted metabolomics studies and it commonly requires extensive processing of more than thousands of metabolite peaks included in raw high-resolution MS data. Although a number of software packages have been developed to facilitate untargeted data processing, they have not been comprehensively scrutinized in the capability of feature detection, quantification and marker selection using a well-defined benchmark sample set. In this study, we acquired a benchmark dataset from standard mixtures consisting of 1100 compounds with specified concentration ratios including 130 compounds with significant variation of concentrations...
October 31, 2018: Analytica Chimica Acta
Anna Marco-Ramell, Sara Tulipani, Magali Palau-Rodriguez, Raul Gonzalez-Dominguez, Antonio Miñarro, Olga Jauregui, Alex Sanchez-Pla, Manuel Macias-Gonzalez, Fernando Cardona, Francisco J Tinahones, Cristina Andres-Lacueva
This study explores the metabolic profiles of concordant/discordant phenotypes of high insulin resistance (IR) and obesity. Through untargeted metabolomics (LC-ESI-QTOF-MS), we analyzed the fasting serum of subjects with high IR and/or obesity ( n = 64). An partial least-squares discriminant analysis with orthogonal signal correction followed by univariate statistics and enrichment analysis allowed exploration of these metabolic profiles. A multivariate regression method (LASSO) was used for variable selection and a predictive biomarker model to identify subjects with high IR regardless of obesity was built...
June 15, 2018: Journal of Proteome Research
Kayla Thomason, Md Ali Babar, John E Erickson, Michael Mulvaney, Chris Beecher, Greg MacDonald
Genetic improvement for stress tolerance requires a solid understanding of biochemical processes involved with different physiological mechanisms and their relationships with different traits. The objective of this study was to demonstrate genetic variability in altered metabolic levels in a panel of six wheat genotypes in contrasting temperature regimes, and to quantify the correlation between those metabolites with different traits. In a controlled environment experiment, heat stress (35:28 ± 0.08°C) was initiated 10 days after anthesis...
2018: PloS One
Boer Xie, Yuanyuan Wang, Drew R Jones, Kaushik Kumar Dey, Xusheng Wang, Yuxin Li, Ji-Hoon Cho, Timothy I Shaw, Haiyan Tan, Junmin Peng
High throughput untargeted metabolomics usually relies on complementary liquid chromatography-mass spectrometry (LC-MS) methods to expand the coverage of diverse metabolites, but the integration of those methods is not fully characterized. We systematically investigated the performance of hydrophilic interaction liquid chromatography (HILIC)-MS and nano-flow reverse phase liquid chromatography (nRPLC)-MS under 8 LC-MS settings, varying stationary phases (HILIC and C18), mobile phases (acidic and basic pH), and MS ionization modes (positive and negative)...
June 8, 2018: Analytical Chemistry
Garth L Maker, Tobias Green, Ian Mullaney, Robert D Trengove
Methamphetamine is an illicit psychostimulant drug that is linked to a number of diseases of the nervous system. The downstream biochemical effects of its primary mechanisms are not well understood, and the objective of this study was to investigate whether untargeted metabolomic analysis of an in vitro model could generate data relevant to what is already known about this drug. Rat B50 neuroblastoma cells were treated with 1 mM methamphetamine for 48 h, and both intracellular and extracellular metabolites were profiled using gas chromatography⁻mass spectrometry...
June 7, 2018: Metabolites
Fang-Hui Li, Tao Li, Jing-Yi Ai, Lei Sun, Zhu Min, Rui Duan, Ling Zhu, Yan-Ying Liu, Timon Cheng-Yi Liu
The effects of high-intensity interval (HIIT) and moderate-intensity continuous training (MICT) on basal autophagy and mitochondrial function in cardiac and skeletal muscle and plasma metabolic phenotypes have not been clearly characterized. Here, we investigated how 10-weeks HIIT and MICT differentially modify basal autophagy and mitochondrial markers in cardiac and skeletal muscle and conducted an untargeted metabolomics study with proton nuclear magnetic resonance (1 H NMR) spectroscopy and multivariate statistical analysis of plasma metabolic phenotypes...
2018: Frontiers in Physiology
Chelsea L Gibson, Simona G Codreanu, Alexandra C Schrimpe-Rutledge, Cassandra L Retzlaff, Jane Wright, Doug P Mortlock, Stacy D Sherrod, John A McLean, Randy D Blakely
The C. elegans gene swip-10 encodes an orphan metallo β-lactamase that genetic studies indicate is vital for limiting neuronal excitability and viability. Sequence analysis indicates that the mammalian gene Mblac1 is the likely ortholog of swip-10, with greatest sequence identity localized to the encoded protein's single metallo β-lactamase domain. The substrate for the SWIP-10 protein remains unknown and to date no functional roles have been ascribed to MBLAC1, though we have shown that the protein binds the neuroprotective β-lactam antibiotic, ceftriaxone...
June 5, 2018: Molecular omics
Yunchen Le, Sulin Zhang, Jiahui Ni, Yan You, Kejing Luo, Yunqiu Yu, Xiaoyan Shen
Amino-acid metabolism plays a vital role in mammalian target of rapamycin (mTOR) signaling, which is the pivot in colorectal cancer (CRC). Upregulated chaperone-mediated autophagy (CMA) activity contributes to the regulation of metabolism in cancer cells. Previously, we found that sorting nexin 10 (SNX10) is a critical regulator in CMA activation. Here we investigated the role of SNX10 in regulating amino-acid metabolism and mTOR signaling pathway activation, as well as the impact on the tumor progression of mouse CRC...
June 4, 2018: Cell Death & Disease
Giorgia Purcaro, Pierre-Hugues Stefanuto, Flavio A Franchina, Marco Beccaria, Wendy F Wieland-Alter, Peter F Wright, Jane E Hill
Untargeted metabolomics study of volatile organic compounds produced by different cell cultures is a field that has gained increasing attention over the years. Solid-phase microextraction has been the sampling technique of choice for most of the applications mainly due to its simplicity to implement. However, a careful optimization of the analytical conditions is necessary to obtain the best performances, which are highly matrix-dependent. In this work, five different solid-phase microextraction fibers were compared for the analysis of the volatiles produced by cell culture infected with the human respiratory syncytial virus...
October 16, 2018: Analytica Chimica Acta
Michael Garratt, Kim A Lagerborg, Yi-Miau Tsai, Andrzej Galecki, Mohit Jain, Richard A Miller
Longevity in mammals is influenced by sex, and lifespan extension in response to anti-aging interventions is often sex-specific, although the mechanisms underlying these sexual dimorphisms are largely unknown. Treatment of mice with 17-α estradiol (17aE2) results in sex-specific lifespan extension, with an increase in median survival in males of 19% and no survival effect in females. Given the links between lifespan extension and metabolism, we performed untargeted metabolomics analysis of liver, skeletal muscle and plasma from male and female mice treated with 17aE2 for eight months...
May 27, 2018: Aging Cell
Yang Wang, Ruibing Feng, Chengwei He, Huanxing Su, Huan Ma, Jian-Bo Wan
The narrow linear range and the limited scan time of the given ion make the quantification of the features challenging in liquid chromatography-mass spectrometry (LC-MS)-based untargeted metabolomics with the full-scan mode. And metabolite identification is another bottleneck of untargeted analysis owing to the difficulty of acquiring MS/MS information of most metabolites detected. In this study, an integrated workflow was proposed using the newly established multiple ion monitoring mode with time-staggered ion lists (tsMIM) and target-directed data-dependent acquisition with time-staggered ion lists (tsDDA) to improve data acquisition and metabolite identification in UHPLC/Q-TOF MS-based untargeted metabolomics...
May 17, 2018: Journal of Pharmaceutical and Biomedical Analysis
Tahira Younis, Mohammad Imran Khan, Muhammad Rashid Khan, Azhar Rasul, Muhammad Majid, Vaqar Mustafa Adhami, Hasan Mukhtar
We recently identified and characterized nummularic acid (NA) as a major chemical constituent of Fraxinus xanthoxyloides, a medicinal plant used for over hundred years in traditional medicine. In this study, we describe its potential anti-cancer activity using prostate cancer (PCa) cells as a model. We found that NA treatment (5-60 μM) significantly reduced the proliferation and colony formation capabilities of PCa DU145 and C4-2 cells in a time and dose dependent manner, reduced the migratory and invasive properties and increased apoptotic cell population...
May 26, 2018: Molecular Carcinogenesis
Lei Wang, Dan Yao, Pedro E Urriola, Andrea R Hanson, Milena Saqui-Salces, Brian J Kerr, Gerald C Shurson, Chi Chen
Consumption of thermally oxidized oil is associated with metabolic disorders, but oxidized oil-elicited changes in the metabolome are not well defined. In this study, C57BL/6 mice were fed the diets containing either control soybean oil or heated soybean oil (HSO) for 4 weeks. HSO-responsive metabolic events were examined through untargeted metabolomics-guided biochemical analysis. HSO directly contributed to the presence of new HSO-derived metabolites in urine and the decrease of polyunsaturated fatty acid-containing phospholipids in serum and the liver...
April 25, 2018: Journal of Nutritional Biochemistry
Jangho Lee, Takayuki Shibamoto, Jaeho Ha, Hae Won Jang
Red ginseng (Panax ginseng) products are frequently adulterated by manufacturers with cheaper medicinal plant products including deodeok (Codonopsis lanceolata) and doraji (Platycodon grandiflorum) to increase profits. To identify possible volatile markers for the adulteration of red ginseng juices with deodeok or doraji, a headspace stir-bar sorptive extraction method was developed. Gas chromatography with mass spectrometry and untargeted metabolomics analysis revealed that 1-hexanol, cis-3-hexen-1-ol, and trans-2-hexen-1-ol are abundantly present in deodeok and doraji but not red ginseng...
May 24, 2018: Journal of Separation Science
Daniel McDonald, Embriette Hyde, Justine W Debelius, James T Morton, Antonio Gonzalez, Gail Ackermann, Alexander A Aksenov, Bahar Behsaz, Caitriona Brennan, Yingfeng Chen, Lindsay DeRight Goldasich, Pieter C Dorrestein, Robert R Dunn, Ashkaan K Fahimipour, James Gaffney, Jack A Gilbert, Grant Gogul, Jessica L Green, Philip Hugenholtz, Greg Humphrey, Curtis Huttenhower, Matthew A Jackson, Stefan Janssen, Dilip V Jeste, Lingjing Jiang, Scott T Kelley, Dan Knights, Tomasz Kosciolek, Joshua Ladau, Jeff Leach, Clarisse Marotz, Dmitry Meleshko, Alexey V Melnik, Jessica L Metcalf, Hosein Mohimani, Emmanuel Montassier, Jose Navas-Molina, Tanya T Nguyen, Shyamal Peddada, Pavel Pevzner, Katherine S Pollard, Gholamali Rahnavard, Adam Robbins-Pianka, Naseer Sangwan, Joshua Shorenstein, Larry Smarr, Se Jin Song, Timothy Spector, Austin D Swafford, Varykina G Thackray, Luke R Thompson, Anupriya Tripathi, Yoshiki Vázquez-Baeza, Alison Vrbanac, Paul Wischmeyer, Elaine Wolfe, Qiyun Zhu, Rob Knight
Although much work has linked the human microbiome to specific phenotypes and lifestyle variables, data from different projects have been challenging to integrate and the extent of microbial and molecular diversity in human stool remains unknown. Using standardized protocols from the Earth Microbiome Project and sample contributions from over 10,000 citizen-scientists, together with an open research network, we compare human microbiome specimens primarily from the United States, United Kingdom, and Australia to one another and to environmental samples...
May 2018: MSystems
William M B Edmands, Josie Hayes, Stephen M Rappaport
Summary: Liquid chromatography mass spectrometry (LC-MS) is the favored method for untargeted metabolomic analysis of small molecules in biofluids. Here we present SimExTargId, an open-source R package for autonomous analysis of metabolomic data and real-time observation of experimental runs. This simultaneous, fully automated and multi-threaded (optional) package is a wrapper for vendor-independent format conversion (ProteoWizard), xcms- and CAMERA- based peak-picking, MetMSLine-based pre-processing and covariate-based statistical analysis...
May 22, 2018: Bioinformatics
Diana Cabrera, Marlena Kruger, Frances M Wolber, Nicole C Roy, John J Totman, Christiani Jeyakumar Henry, David Cameron-Smith, Karl Fraser
The diagnosis of osteoporosis is mainly based on clinical examination and bone mineral density assessments. The present pilot study compares the plasma lipid and polar metabolite profiles in blood plasma of 95 Singaporean-Chinese (SC) menopausal women with normal and low bone mineral density (BMD) using an untargeted metabolomic approach. The primary finding of this study was the association between lipids and femoral neck BMD in SC menopausal women. Twelve lipids were identified to be associated with low BMD by the orthogonal partial least squares (OPLS) model...
May 22, 2018: International Journal of Environmental Research and Public Health
Grégory Pimentel, Kathryn J Burton, Ueli von Ah, Ueli Bütikofer, François P Pralong, Nathalie Vionnet, Reto Portmann, Guy Vergères
Background: Fermentation is a widely used method of natural food preservation that has consequences on the nutritional value of the transformed food. Fermented dairy products are increasingly investigated in view of their ability to exert health benefits beyond their nutritional qualities. Objective: To explore the mechanisms underpinning the health benefits of fermented dairy intake, the present study followed the effects of milk fermentation, from changes in the product metabolome to consequences on the human serum metabolome after its ingestion...
May 21, 2018: Journal of Nutrition
Kota Kera, Dennis D Fine, Daniel J Wherritt, Yoshiki Nagashima, Norimoto Shimada, Takeshi Ara, Yoshiyuki Ogata, Lloyd W Sumner, Hideyuki Suzuki
Introduction: Oxygen from carbon dioxide, water or molecular oxygen, depending on the responsible enzyme, can lead to a large variety of metabolites through chemical modification. Objectives: Pathway-specific labeling using isotopic molecular oxygen (18 O2 ) makes it possible to determine the origin of oxygen atoms in metabolites and the presence of biosynthetic enzymes (e.g., oxygenases). In this study, we established the basis of 18 O2 -metabolome analysis. Methods: 18 O2 labeled whole Medicago truncatula seedlings were prepared using 18 O2 -air and an economical sealed-glass bottle system...
2018: Metabolomics: Official Journal of the Metabolomic Society
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