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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/29453510/next-generation-metabolic-screening-targeted-and-untargeted-metabolomics-for-the-diagnosis-of-inborn-errors-of-metabolism-in-individual-patients
#1
Karlien L M Coene, Leo A J Kluijtmans, Ed van der Heeft, Udo F H Engelke, Siebolt de Boer, Brechtje Hoegen, Hanneke J T Kwast, Maartje van de Vorst, Marleen C D G Huigen, Irene M L W Keularts, Michiel F Schreuder, Clara D M van Karnebeek, Saskia B Wortmann, Maaike C de Vries, Mirian C H Janssen, Christian Gilissen, Jasper Engel, Ron A Wevers
The implementation of whole-exome sequencing in clinical diagnostics has generated a need for functional evaluation of genetic variants. In the field of inborn errors of metabolism (IEM), a diverse spectrum of targeted biochemical assays is employed to analyze a limited amount of metabolites. We now present a single-platform, high-resolution liquid chromatography quadrupole time of flight (LC-QTOF) method that can be applied for holistic metabolic profiling in plasma of individual IEM-suspected patients. This method, which we termed "next-generation metabolic screening" (NGMS), can detect >10,000 features in each sample...
February 16, 2018: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/29453063/-1-h-nmr-based-metabolomics-reveals-interactive-effects-between-the-carrier-solvent-methanol-and-a-pharmaceutical-mixture-in-an-amphibian-developmental-bioassay-with-limnodynastes-peronii
#2
Steven D Melvin, Oliver A H Jones, Anthony R Carroll, Frederic D L Leusch
Organic carrier solvents are used in aquatic toxicity testing to improve chemical solubility and facilitate the exploration of dose-response relationships. Both water- and solvent-control groups are normally included in these scenarios to ensure that the solvent itself has no effect on the test organism, but this fails to consider possible interactive effects between carrier solvents and contaminants of interest. We explored this topic by exposing Limnodynastes peronii tadpoles to a mixture of common water-soluble pharmaceuticals (diclofenac, metformin and valproic acid) in the presence and absence of the carrier solvent methanol, according to standard developmental bioassay methodology...
February 10, 2018: Chemosphere
https://www.readbyqxmd.com/read/29453015/metabolomic-profiling-of-campylobacter-jejuni-with-resistance-gene-ermb-by-ultra-high-performance-liquid-chromatography-quadrupole-time-of-flight-mass-spectrometry-and-tandem-quadrupole-mass-spectrometry
#3
Qin Fu, Dejun Liu, Yingyu Wang, Xiaowei Li, Lina Wang, Fugen Yu, Jianzhong Shen, Xi Xia
The metabolome changes of Campylobacter jejuni with resistant gene ermB remain unclear. Here, we described an untargeted metabolomic workflow based on ultra-high performance liquid chromatography-quadrupole time-of-flight mass spectrometry to investigate the metabolites perturbations mediated by ermB in C. jejuni. After optimization of extractants and chromatographic conditions, the combination of 100% methanol extraction with a 12 min gradient by C18 column was adopted for untargeted metabolomic profiling in reversed phase separation...
February 10, 2018: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/29438325/untargeted-metabolomics-profiling-of-an-80-5-km-simulated-treadmill-ultramarathon
#4
Christopher C F Howe, Ahmed Alshehri, David Muggeridge, Alexander B Mullen, Marie Boyd, Owen Spendiff, Hannah J Moir, David G Watson
Metabolomic profiling of nine trained ultramarathon runners completing an 80.5 km self-paced treadmill-based time trial was carried out. Plasma samples were obtained from venous whole blood, collected at rest and on completion of the distance (post-80.5 km). The samples were analyzed by using high-resolution mass spectrometry in combination with both hydrophilic interaction (HILIC) and reversed phase (RP) chromatography. The extracted putatively identified features were modeled using Simca P 14.1 software (Umetrics, Umea, Sweden)...
February 13, 2018: Metabolites
https://www.readbyqxmd.com/read/29436716/chemocoding-as-an-identification-tool-where-morphological-and-dna-based-methods-fall-short-inga-as-a-case-study
#5
María-José Endara, Phyllis D Coley, Natasha L Wiggins, Dale L Forrister, Gordon C Younkin, James A Nicholls, R Toby Pennington, Kyle G Dexter, Catherine A Kidner, Graham N Stone, Thomas A Kursar
The need for species identification and taxonomic discovery has led to the development of innovative technologies for large-scale plant identification. DNA barcoding has been useful, but fails to distinguish among many species in species-rich plant genera, particularly in tropical regions. Here, we show that chemical fingerprinting, or 'chemocoding', has great potential for plant identification in challenging tropical biomes. Using untargeted metabolomics in combination with multivariate analysis, we constructed species-level fingerprints, which we define as chemocoding...
February 13, 2018: New Phytologist
https://www.readbyqxmd.com/read/29430917/untargeted-metabolomics-reveal-lipid-alterations-upon-2-deoxyglucose-treatment-in-human-hacat-keratinocytes
#6
Pierre Le Pogam, Mickaël Doué, Yann Le Page, Denis Habauzit, Maxim Zhadobov, Ronan Sauleau, Yves Le Dréan, David Rondeau
The glucose-analogue 2-deoxyglucose (2-DG) impedes cancer progression in animal models and is currently being assessed as an anti-cancer therapy. Yet, the mode of action of this drug of high clinical significance has not been fully delineated. In an attempt to better characterize its pharmacodynamics, an integrative UPLC-Q-Exactive based joint metabolomic and lipidomic approach was undertaken to evaluate the metabolic perturbations induced by this drug in human HaCaT keratinocyte cells. R-XCMS data processing and subsequent multivariate pattern recognition, metabolites identification and pathway analyses identified 8 metabolites that were most significantly changed upon a 3 h 2-DG exposure...
February 12, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29425452/evaluation-of-the-high-field-orbitrap-fusion-for-compound-annotation-in-metabolomics
#7
Pierre Barbier Saint Hilaire, Ulli M Hohenester, Benoit Colsch, Jean-Claude Tabet, Christophe Junot, François Fenaille
Annotation of signals of interest represents a key point in mass spectrometry-based metabolomics studies. The first level of investigation is the elemental composition, that can be deduced from accurately measured masses and isotope patterns. However, accuracy of these two parameters remains to be evaluated on last generation mass spectrometers to determine the level of confidence that can be used during the annotation process. In this context, we evaluated the performance of the Orbitrap Fusion mass spectrometer for the first time and demonstrated huge potential for metabolite annotation via elemental composition determination...
February 9, 2018: Analytical Chemistry
https://www.readbyqxmd.com/read/29423831/targeted-versus-untargeted-omics-the-cafsa-story
#8
Maria Del Mar Amador, Benoit Colsch, Foudil Lamari, Claude Jardel, Farid Ichou, Agnès Rastetter, Frédéric Sedel, Fabien Jourdan, Clément Frainay, Ronald A Wevers, Emmanuel Roze, Christel Depienne, Christophe Junot, Fanny Mochel
BACKGROUND: In 2009, untargeted metabolomics led to the delineation of a new clinico-biological entity called cerebellar ataxia with elevated cerebrospinal free sialic acid, or CAFSA. In order to elucidate CAFSA, we applied sequentially targeted and untargeted omic approaches. METHODS AND RESULTS: First, we studied five of the six CAFSA patients initially described. Besides increased CSF free sialic acid concentrations, three patients presented with markedly decreased 5-methyltetrahydrofolate (5-MTHF) CSF concentrations...
February 8, 2018: Journal of Inherited Metabolic Disease
https://www.readbyqxmd.com/read/29419819/a-metabolomic-map-of-zellweger-spectrum-disorders-reveals-novel-disease-biomarkers
#9
Michael F Wangler, Leroy Hubert, Taraka R Donti, Meredith J Ventura, Marcus J Miller, Nancy Braverman, Kelly Gawron, Mousumi Bose, Ann B Moser, Richard O Jones, William B Rizzo, V Reid Sutton, Qin Sun, Adam D Kennedy, Sarah H Elsea
PurposePeroxisome biogenesis disorders-Zellweger spectrum disorders (PBD-ZSD) are metabolic diseases with multisystem manifestations. Individuals with PBD-ZSD exhibit impaired peroxisomal biochemical functions and have abnormal levels of peroxisomal metabolites, but the broader metabolic impact of peroxisomal dysfunction and the utility of metabolomic methods is unknown.MethodsWe studied 19 individuals with clinically and molecularly characterized PBD-ZSD. We performed both quantitative peroxisomal biochemical diagnostic studies in parallel with untargeted small molecule metabolomic profiling in plasma samples with detection of >650 named compounds...
February 8, 2018: Genetics in Medicine: Official Journal of the American College of Medical Genetics
https://www.readbyqxmd.com/read/29417056/untargeted-metabolomics-confirms-and-extends-the-understanding-of-the-impact-of-aminoimidazole-carboxamide-ribotide-aicar-in-the-metabolic-network-of-salmonella-enterica
#10
Jannell V Bazurto, Stephen P Dearth, Eric D Tague, Shawn R Campagna, Diana M Downs
In Salmonella enterica, aminoimidazole carboxamide ribotide (AICAR) is a purine biosynthetic intermediate and a substrate of the AICAR transformylase/IMP cyclohydrolase (PurH) enzyme. When purH is eliminated in an otherwise wild-type strain, AICAR accumulates and indirectly inhibits synthesis of the essential coenzyme thiamine pyrophosphate (TPP). In this study, untargeted metabolomics approaches were used to i) corroborate previously defined metabolite changes, ii) define the global consequences of AICAR accumulation and iii) investigate the metabolic effects of mutations that restore thiamine prototrophy to a purH mutant...
November 22, 2017: Microbial Cell
https://www.readbyqxmd.com/read/29413971/-gear-mechanism-of-bariatric-interventions-revealed-by-untargeted-metabolomics
#11
Paulina Samczuk, Magdalena Luba, Joanna Godzien, Annalaura Mastrangelo, Hady Razak Hady, Jacek Dadan, Coral Barbas, Maria Gorska, Adam Kretowski, Michal Ciborowski
Mechanisms responsible for metabolic gains after bariatric surgery are not entirely clear. The purpose of this study was evaluation of metabolic changes after laparoscopic Roux-en-Y gastric bypass or laparoscopic sleeve gastrectomy in semi-annual follow up. The study participants were selected from obese patients with T2DM who underwent one of the mentioned bariatric procedures. Serum metabolic fingerprinting by use of liquid and gas chromatography with mass spectrometry detection was performed on samples obtained from studied patients before, one, and six months post-surgery...
January 9, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29413746/advances-in-computational-metabolomics-and-databases-deepen-the-understanding-of-metabolisms
#12
REVIEW
Hiroshi Tsugawa
Mass spectrometry (MS)-based metabolomics is the popular platform for metabolome analyses. Computational techniques for the processing of MS raw data, for example, feature detection, peak alignment, and the exclusion of false-positive peaks, have been established. The next stage of untargeted metabolomics would be to decipher the mass fragmentation of small molecules for the global identification of human-, animal-, plant-, and microbiota metabolomes, resulting in a deeper understanding of metabolisms. This review is an update on the latest computational metabolomics including known/expected structure databases, chemical ontology classifications, and mass spectrometry cheminformatics for the interpretation of mass fragmentations and for the elucidation of unknown metabolites...
January 29, 2018: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/29412933/assessment-of-protected-designation-of-origin-for-colombian-coffees-based-on-hrms-based-metabolomics
#13
Duvan E Hoyos Ossa, Rubén Gil-Solsona, Gustavo A Peñuela, Juan Vicente Sancho, Felix J Hernández
An untargeted metabolomics approach based on HRMS has been applied to Colombian green coffee to develop a discrimination model to highlight the most differential compounds. For this purpose, 41 green coffee samples of different genotypes collected from 5 regions were analysed. Samples were extracted with aqueous and organic solvents to cover a wide range of compounds. Sample extracts were randomly injected and data were pre-processed with XCMS software. PCA was used to verify quality control samples behaviour, and PLS-DA and DD-SIMCA were employed to create models for discrimination using VIP variable selection method...
June 1, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29407911/label-free-proteomic-analysis-to-characterize-ginger-from-china-and-ghana
#14
Xiaojian Yin, Shi-Lei Wang, Raphael N Alolga, Enos Mais, Ping Li, Pingfang Yang, Setsuko Komatsu, Lian-Wen Qi
Ginger is a popular spice used in food and beverages. In this study, we sought to characterize and differentiate ginger samples of Ghana and China origin using label-free proteomic and untargeted metabolomic analyses. As result, a total of 180 proteins significantly changed between the ginger samples from both studied countries. Among them, 17 proteins were specifically identified in the Chinese ginger, while 23 proteins were only identified in the Ghanaian ginger. Function and bioinformatics analyses indicated that changes in carbon metabolism, secondary metabolites biosyntheses, citrate acid cycle, and amino acids biosyntheses-related pathways contributed to the differences...
May 30, 2018: Food Chemistry
https://www.readbyqxmd.com/read/29384544/from-genomics-to-metabolomics-moving-toward-an-integrated-strategy-for-the-discovery-of-fungal-secondary-metabolites
#15
REVIEW
T Hautbergue, E L Jamin, L Debrauwer, O Puel, I P Oswald
Fungal secondary metabolites are defined by bioactive properties that ensure adaptation of the fungus to its environment. Although some of these natural products are promising sources of new lead compounds especially for the pharmaceutical industry, others pose risks to human and animal health. The identification of secondary metabolites is critical to assessing both the utility and risks of these compounds. Since fungi present biological specificities different from other microorganisms, this review covers the different strategies specifically used in fungal studies to perform this critical identification...
January 31, 2018: Natural Product Reports
https://www.readbyqxmd.com/read/29377494/untargeted-metabolomic-screen-reveals-changes-in-human-plasma-metabolite-profiles-following-consumption-of-fresh-broccoli-sprouts
#16
Lauren Housley, Armando Alcazar Magana, Anna Hsu, Laura M Beaver, Carmen P Wong, Jan F Stevens, Jaewoo Choi, Yuan Jiang, Deborah Bella, David E Williams, Claudia S Maier, Jackilen Shannon, Roderick H Dashwood, Emily Ho
SCOPE: Several lines of evidence suggest that the consumption of cruciferous vegetables is beneficial to human health. Yet, underlying mechanisms and key molecular targets that are involved with achieving these benefits in humans are still not fully understood. To accelerate this research, we conducted a human study to identify potential molecular targets of crucifers for further study. This study aimed to characterize plasma metabolite profiles in humans before and after consuming fresh broccoli sprouts (a rich dietary source of bioactive sulforaphane)...
January 28, 2018: Molecular Nutrition & Food Research
https://www.readbyqxmd.com/read/29373032/tissue-level-diet-and-sex-by-diet-interactions-reveal-unique-metabolite-and-clustering-profiles-using-untargeted-liquid-chromatography-mass-spectrometry-on-adipose-skeletal-muscle-and-liver-tissue-in-c57bl6-j-mice
#17
Ann Wells, William T Barrington, Stephen Dearth, Amanda May, David W Threadgill, Shawn R Campagna, Brynn H Voy
Dietary intervention is commonly used for weight loss or to improve health, as diet-induced obesity increases risk of developing type 2 diabetes, hypertension, cardiovascular disease, stroke, osteoarthritis, and certain cancers. Various dietary patterns are associated with effects on health, yet little is known about the effects of diet at the tissue level. Using untargeted metabolomics, this study aimed to identify changes in water-soluble metabolites in C57BL/6J males and females, fed one of five diets (Japanese, ketogenic, Mediterranean, American, and standard mouse chow) for seven months...
January 26, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29372429/exploring-traditional-aus-type-rice-for-metabolites-conferring-drought-tolerance
#18
Alberto Casartelli, David Riewe, Hans Michael Hubberten, Thomas Altmann, Rainer Hoefgen, Sigrid Heuer
BACKGROUND: Traditional varieties and landraces belonging to the aus-type group of rice (Oryza sativa L.) are known to be highly tolerant to environmental stresses, such as drought and heat, and are therefore recognized as a valuable genetic resource for crop improvement. Using two aus-type (Dular, N22) and two drought intolerant irrigated varieties (IR64, IR74) an untargeted metabolomics analysis was conducted to identify drought-responsive metabolites associated with tolerance. RESULTS: The superior drought tolerance of Dular and N22 compared with the irrigated varieties was confirmed by phenotyping plants grown to maturity after imposing severe drought stress in a dry-down treatment...
January 25, 2018: Rice
https://www.readbyqxmd.com/read/29365091/nmr-metabolomic-signatures-reveal-predictive-plasma-metabolites-associated-with-long-term-risk-of-developing-breast-cancer
#19
Lucie Lécuyer, Agnès Victor Bala, Mélanie Deschasaux, Nadia Bouchemal, Mohamed Nawfal Triba, Marie-Paule Vasson, Adrien Rossary, Aicha Demidem, Pilar Galan, Serge Hercberg, Valentin Partula, Laurence Le Moyec, Bernard Srour, Thibault Fiolet, Paule Latino-Martel, Emmanuelle Kesse-Guyot, Philippe Savarin, Mathilde Touvier
Background: Combination of metabolomics and epidemiological approaches opens new perspectives for ground-breaking discoveries. The aim of the present study was to investigate for the first time whether plasma untargeted metabolomic profiles, established from a simple blood draw from healthy women, could contribute to predict the risk of developing breast cancer within the following decade and to better understand the aetiology of this complex disease. Methods: A prospective nested case-control study was set up in the Supplémentation en Vitamines et Minéraux Antioxydants (SU...
January 19, 2018: International Journal of Epidemiology
https://www.readbyqxmd.com/read/29363077/exploratory-gc-ms-based-metabolomics-of-body-fluids
#20
Carole Migné, Stéphanie Durand, Estelle Pujos-Guillot
GC/MS-based metabolomics is a powerful tool for metabolic phenotyping and biomarker discovery from body biofluids. In this chapter, we describe an untargeted metabolomic approach for plasma/serum and fecal water sample profiling. It describes a multistep procedure, from sample preparation, oximation/silylation derivatization, and data acquisition using GC/QToF to data processing consisting in data extraction and identification of metabolites.
2018: Methods in Molecular Biology
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