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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/28424615/huangqin-decoction-attenuates-cpt-11-induced-gastrointestinal-toxicity-by-regulating-bile-acids-metabolism-homeostasis
#1
Xu Wang, Dong-Ni Cui, Xiao-Min Dai, Jing Wang, Wei Zhang, Zun-Jian Zhang, Feng-Guo Xu
Irinotecan (CPT-11) is a potent chemotherapeutic agent, however, its clinical usage is often limited by the induction of severe gastrointestinal (GI) toxicity, especially late-onset diarrhea. HuangQin Decoction (HQD), commonly used for the treatment of GI ailments, has been proved could significantly ameliorate the intestinal toxicity of CPT-11. To reveal the mechanisms of CPT-11-induced toxicity and the modulation effects of HQD, a previous untargeted metabolomics study was performed and the results indicated that HQD may protect the GI tract by altering the metabolism of bile acids (BAs)...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28402628/influences-of-normalization-method-on-biomarker-discovery-in-gas-chromatography-mass-spectrometry-based-untargeted-metabolomics-what-should-be-considered
#2
Jiaqing Chen, Pei Zhang, Mengying Lv, Huimin Guo, Yin Huang, Zunjian Zhang, Fengguo Xu
Data reduction techniques in Gas Chromatography-Mass Spectrometry based untargeted metabolomics has made the following workflow of data analysis more lucid. However, the normalization process still perplexes researchers and its effects are always ignored. In order to reveal the influences of normalization method, five representative normalization methods (Mass Spectrometry Total Useful Signal, Median, Probabilistic Quotient Normalization, Remove Unwanted Variation-random and Systematic Ratio Normalization) were compared in three real datasets with different types...
April 12, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28401628/metabolomics-reveals-new-metabolic-perturbations-in-children-with-type-1-diabetes
#3
Alfonso Galderisi, Paola Pirillo, Vittoria Moret, Matteo Stocchero, Antonina Gucciardi, Giorgio Perilongo, Carlo Moretti, Carlamaria Monciotti, Giuseppe Giordano, Eugenio Baraldi
OBJECTIVE: Using an untargeted metabolomics approach we investigated the metabolome of children with type 1 diabetes (T1D) in comparison with healthy peers and explored the contribution of HbA1c and clinical features to the observed difference. RESEARCH DESIGN AND METHODS: We enrolled children with T1D aged 6-15 years, attending the pediatric diabetes clinic of University of Padova (Italy). Healthy controls were enrolled on voluntary basis and matched for age, sex, pubertal status, body mass index (BMI)...
April 12, 2017: Pediatric Diabetes
https://www.readbyqxmd.com/read/28391692/customized-consensus-spectral-library-building-for-untargeted-quantitative-metabolomics-analysis-with-data-independent-acquisition-mass-spectrometry-and-metabodia-workflow
#4
Gengbo Chen, Scott Walmsley, Gemmy C M Cheung, Liyan Chen, Ching-Yu Cheng, Roger W Beuerman, Tien Yin Wong, Lei Zhou, Hyungwon Choi
Data independent acquisition-mass spectrometry (DIA-MS) coupled with liquid chromatography is a promising approach for rapid, automatic sampling of MS/MS data in untargeted metabolomics. However, wide isolation windows in DIA-MS generate MS/MS spectra containing a mixed population of fragment ions together with their precursor ions. This precursor-fragment ion map in a comprehensive MS/MS spectral library is crucial for relative quantification of fragment ions uniquely representative of each precursor ion. However, existing reference libraries are not sufficient for this purpose since the fragmentation patterns of small molecules can vary in different instrument setups...
April 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28390668/strategy-for-comparative-untargeted-metabolomics-reveals-honey-markers-of-different-floral-and-geographic-origins-using-ultrahigh-performance-liquid-chromatography-hybrid-quadrupole-orbitrap-mass-spectrometry
#5
Yi Li, Yue Jin, Shupeng Yang, Wenwen Zhang, Jinzhen Zhang, Wen Zhao, Lanzhen Chen, Yaqin Wen, Yongxin Zhang, Kaizhi Lu, Yaping Zhang, Jinhui Zhou, Shuming Yang
Honey discrimination based on floral and geographic origins is limited by the ability to determine reliable markers because developing hypothetical substances in advance considerably limits the throughput of metabolomics studies. Here, we present a novel approach to screen and elucidate honey markers based on comparative untargeted metabolomics using ultrahigh-performance liquid chromatography-hybrid quadrupole-orbitrap mass spectrometry (UHPLC-Q-Orbitrap). To reduce metabolite information losses during sample preparation, the honey samples were dissolved in water and centrifuged to remove insoluble particles prior to UHPLC-Q-Orbitrap analysis in positive and negative electrospray ionization modes...
March 28, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28378853/serum-metabolomic-profiling-highlights-pathways-associated-with-liver-fat-content-in-a-general-population-sample
#6
M Koch, S Freitag-Wolf, S Schlesinger, J Borggrefe, J R Hov, M K Jensen, J Pick, M R P Markus, T Höpfner, G Jacobs, S Siegert, A Artati, G Kastenmüller, W Römisch-Margl, J Adamski, T Illig, M Nothnagel, T H Karlsen, S Schreiber, A Franke, M Krawczak, U Nöthlings, W Lieb
BACKGROUND/OBJECTIVES: Fatty liver disease (FLD) is an important intermediate trait along the cardiometabolic disease spectrum and strongly associates with type 2 diabetes. Knowledge of biological pathways implicated in FLD is limited. An untargeted metabolomic approach might unravel novel pathways related to FLD. SUBJECTS/METHODS: In a population-based sample (n=555) from Northern Germany, liver fat content was quantified as liver signal intensity using magnetic resonance imaging...
April 5, 2017: European Journal of Clinical Nutrition
https://www.readbyqxmd.com/read/28367722/feline-urine-metabolomic-signature-characterization-of-low-molecular-weight-substances-in-urine-from-domestic-cats
#7
Sol-Maiam Rivera-Vélez, Nicolas F Villarino
Objectives This aim of this study was to characterize the composition and content of the feline urine metabolome. Methods Eight healthy domestic cats were acclimated at least 10 days before starting the study. Urine samples (~2 ml) were collected by ultrasound-guided cystocentesis. Samples were centrifuged at 1000 × g for 8 mins, and the supernatant was analyzed by gas chromatography/time-of-flight mass spectrometery. The urine metabolome was characterized using an untargeted metabolomics approach. Results Three hundred and eighteen metabolites were detected in the urine of the eight cats...
March 1, 2017: Journal of Feline Medicine and Surgery
https://www.readbyqxmd.com/read/28365236/the-assessment-of-the-chronic-hepatotoxicity-induced-by-polygoni-multiflori-radix-in-rats-a-pilot-study-by-using-untargeted-metabolomics-method
#8
Xin-Hua Xia, Yuan-Yuan Yuan, Mei Liu
Polygoni Multiflori Radix is the dried root of Polygonum multiflorum Thunb officially recorded in the Chinese Pharmacopoeia as HeShouWu (HSW) in Chinese pinyin. The processed HSW are commonly used in TCM to treat liver disease and Chinese Pharmacopoeia has described the actions of it to tonify liver-kidney, replenish essence and blood, blacken beard and hair, strengthen sinew and bone, and resolve turbidity and lower lipid hence making it use not only as a herbal medicine in TCM but also as supplementary food in health care...
March 29, 2017: Journal of Ethnopharmacology
https://www.readbyqxmd.com/read/28358014/untargeted-metabolomics-analysis-reveals-key-pathways-responsible-for-the-synergistic-killing-of-colistin-and-doripenem-combination-against-acinetobacter-baumannii
#9
Mohd Hafidz Mahamad Maifiah, Darren J Creek, Roger L Nation, Alan Forrest, Brian T Tsuji, Tony Velkov, Jian Li
Combination therapy is deployed for the treatment of multidrug-resistant Acinetobacter baumannii, as it can rapidly develop resistance to current antibiotics. This is the first study to investigate the synergistic effect of colistin/doripenem combination on the metabolome of A. baumannii. The metabolite levels were measured using LC-MS following treatment with colistin (2 mg/L) or doripenem (25 mg/L) alone, and their combination at 15 min, 1 hr and 4 hr (n = 4). Colistin caused early (15 min and 1 hr) disruption of the bacterial outer membrane and cell wall, as demonstrated by perturbation of glycerophospholipids and fatty acids...
March 30, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28351740/evidencing-98-secondary-metabolites-of-penicillium-verrucosum-using-substrate-isotopic-labeling-and-high-resolution-mass-spectrometry
#10
Thaïs Hautbergue, Olivier Puel, Souria Tadrist, Lauriane Meneghetti, Michel Péan, Marcel Delaforge, Laurent Debrauwer, Isabelle P Oswald, Emilien L Jamin
Industrial applications of fungal compounds, coupled with the emergence of fungal threats to natural ecosystems and public health, have increased interest in filamentous fungi. Among all pathogenic fungi, Penicillium verrucosum is one of the most common mold-infecting stored cereals in temperate regions. However, it is estimated that 80% of fungal secondary metabolites remain unknown. To detect new P. verrucosum compounds, an untargeted metabolomic approach was applied to fungus grown on wheat grains labeled with stable isotopes: (i) natural grains (99% (12)C); (ii) grains enriched with 97% of (13)C; and (iii) grains enriched with 53% of (13)C and 97% of (15)N...
March 12, 2017: Journal of Chromatography. B, Analytical Technologies in the Biomedical and Life Sciences
https://www.readbyqxmd.com/read/28351639/untargeted-assignment-and-automatic-integration-of-1-h-nmr-metabolomic-datasets-using-a-multivariate-curve-resolution-approach
#11
Francesc Puig-Castellví, Ignacio Alfonso, Romà Tauler
In this article, we propose the use of the Multivariate Curve Resolution - Alternating Least Squares (MCR-ALS) chemometrics method to resolve the (1)H NMR spectra and concentration of the individual metabolites in their mixtures in untargeted metabolomics studies. A decision tree-based strategy is presented to optimally select and implement spectra estimates and equality constraints during MCR-ALS optimization. The proposed method has been satisfactorily evaluated using different (1)H NMR metabolomics datasets...
April 29, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28344557/dissecting-target-toxic-tissue-and-tissue-specific-responses-of-irinotecan-in-rats-using-metabolomics-approach
#12
Yiran Yao, Pei Zhang, Jing Wang, Jiaqing Chen, Yong Wang, Yin Huang, Zunjian Zhang, Fengguo Xu
As an anticancer agent, irinotecan (CPT-11) has been widely applied in clinical, especially in the treatment of colorectal cancer. However, its clinical use has long been limited by the side effects and potential tissue toxicity. To discriminate the target toxic tissues and dissect the specific response of target tissues after CPT-11 administration in rats, untargeted metabolomic study was conducted. First, differential metabolites between CPT-11 treated group and control group in each tissue were screened out...
2017: Frontiers in Pharmacology
https://www.readbyqxmd.com/read/28321230/integrated-transcriptome-and-metabolic-analyses-reveals-novel-insights-into-free-amino-acid-metabolism-in-huangjinya-tea-cultivar
#13
Qunfeng Zhang, Meiya Liu, Jianyun Ruan
The chlorotic tea variety Huangjinya, a natural mutant, contains enhanced levels of free amino acids in its leaves, which improves the drinking quality of its brewed tea. Consequently, this chlorotic mutant has a higher economic value than the non-chlorotic varieties. However, the molecular mechanisms behind the increased levels of free amino acids in this mutant are mostly unknown, as are the possible effects of this mutation on the overall metabolome and biosynthetic pathways in tea leaves. To gain further insight into the effects of chlorosis on the global metabolome and biosynthetic pathways in this mutant, Huangjinya plants were grown under normal and reduced sunlight, resulting in chlorotic and non-chlorotic leaves, respectively; their leaves were analyzed using transcriptomics as well as targeted and untargeted metabolomics...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28316657/comprehensive-identification-of-sphingolipid-species-by-in-silico-retention-time-and-tandem-mass-spectral-library
#14
Hiroshi Tsugawa, Kazutaka Ikeda, Wataru Tanaka, Yuya Senoo, Makoto Arita, Masanori Arita
BACKGROUND: Liquid chromatography coupled with electrospray ionization tandem mass spectrometry (LC-ESI-MS/MS) is used for comprehensive metabolome and lipidome analyses. Compound identification relies on similarity matching of the retention time (RT), precursor m/z, isotopic ratio, and MS/MS spectrum with reference compounds. For sphingolipids, however, little information on the RT and MS/MS references is available. RESULTS: Negative-ion ESI-MS/MS is a useful method for the structural characterization of sphingolipids...
2017: Journal of Cheminformatics
https://www.readbyqxmd.com/read/28300186/renal-medulla-is-more-sensitive-to-cisplatin-than-cortex-revealed-by-untargeted-mass-spectrometry-based-metabolomics-in-rats
#15
Pei Zhang, Jia-Qing Chen, Wan-Qiu Huang, Wei Li, Yin Huang, Zun-Jian Zhang, Feng-Guo Xu
Nephrotoxicity has long been the most severe and life-threatening side-effect of cisplatin, whose anticancer effect is therefore restricted. Previous pathological studies have shown that both renal cortex and medulla could be injured by cisplatin. Our TUNEL (terminal deoxynucleotidyl transferase-mediated dUTP nick end-labeling) assay results further uncovered that medulla subjected more severe injury than cortex. In order to depict the underlying metabolic mechanism of spatial difference in response to cisplatin, in the present study, mass spectrometry-based untargeted metabolomics approach was applied to profile renal cortex and medulla metabolites of rat after receiving a single dose of cisplatin (2...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28290675/development-of-untargeted-metabolomics-methods-for-the-rapid-detection-of-pathogenic-naegleria-fowleri
#16
Zhihao Yu, Haylea C Miller, Geoffrey J Puzon, Brian H Clowers
Despite comparatively low levels of infection, primary amoebic meningoencephalitis (PAM) induced by Naegleria fowleri is extremely lethal, with mortality rates above 95%. As a thermophile, this organism is often found in moderate-to-warm climates and has the potential to colonize drinking water distribution systems (DWDSs). Current detection approaches require days to obtain results, whereas swift corrective action can maximize the benefit of public health. Presently, there is little information regarding the underlying in situ metabolism for this amoeba but the potential exists to exploit differentially expressed metabolic signatures as a rapid detection technique...
March 29, 2017: Environmental Science & Technology
https://www.readbyqxmd.com/read/28283295/global-metabolome-changes-induced-by-cyanobacterial-blooms-in-three-representative-fish-species
#17
Benoît Sotton, Alain Paris, Séverine Le Manach, Alain Blond, Gérard Lacroix, Alexis Millot, Charlotte Duval, Qin Qiao, Arnaud Catherine, Benjamin Marie
Cyanobacterial blooms induce important ecological constraints for aquatic organisms and strongly impact the functioning of aquatic ecosystems. In the past decades, the effects of the cyanobacterial secondary metabolites, so called cyanotoxins, have been extensively studied in fish. However, many of these studies have used targeted approaches on specific molecules, which are thought to react to the presence of these specific cyanobacterial compounds. Since a few years, untargeted metabolomic approaches provide a unique opportunity to evaluate the global response of hundreds of metabolites at a glance...
July 15, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28272510/apolipoprotein-e4-and-insulin-resistance-interact-to-impair-cognition-and-alter-the-epigenome-and-metabolome
#18
Lance A Johnson, Eileen Ruth S Torres, Soren Impey, Jan F Stevens, Jacob Raber
Apolipoprotein E4 (E4) and type 2 diabetes are major risk factors for cognitive decline and late onset Alzheimer's disease (AD). E4-associated phenotypes and insulin resistance (IR) share several features and appear to interact in driving cognitive dysfunction. However, shared mechanisms that could explain their overlapping pathophysiology have yet to be found. We hypothesized that, compared to E3 mice, E4 mice would be more susceptible to the harmful cognitive effects of high fat diet (HFD)-induced IR due to apoE isoform-specific differences in brain metabolism...
March 8, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28271897/branched-chain-amino-acids-as-predictors-for-individual-differences-of-cisplatin-nephrotoxicity-in-rats-a-pharmacometabonomics-study
#19
Pei Zhang, Wei Li, Jiaqing Chen, Ruiting Li, Zunjian Zhang, Yin Huang, Fengguo Xu
Nephrotoxicity is the dose-limiting adverse effect of cisplatin with large individual differences. Up to now, little has been done on how to recognize and predict the individual differences in either preclinical or clinical research. In the present study, important postdose indicators were screened out first and integrated into a grouping factor, according to which rats were recognized as lowly or highly sensitive individuals. Then, mass-spectrometry-based untargeted metabolomics approach was performed to dissect the metabolic differences in predose serum of the two groups...
March 17, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28264975/endogenous-and-xenobiotic-metabolic-stability-of-primary-human-hepatocytes-in-long-term-3d-spheroid-cultures-revealed-by-a-combination-of-targeted-and-untargeted-metabolomics
#20
Sabine U Vorrink, Shahid Ullah, Staffan Schmidt, Jatin Nandania, Vidya Velagapudi, Olof Beck, Magnus Ingelman-Sundberg, Volker M Lauschke
Adverse reactions or lack of response to medications are important concerns for drug development programs. However, faithful predictions of drug metabolism and toxicity are difficult because animal models show only limited translatability to humans. Furthermore, current in vitro systems, such as hepatic cell lines or primary human hepatocyte (PHH) 2-dimensional (2D) monolayer cultures, can be used only for acute toxicity tests because of their immature phenotypes and inherent instability. Therefore, the migration to novel phenotypically stable models is of prime importance for the pharmaceutical industry...
March 6, 2017: FASEB Journal: Official Publication of the Federation of American Societies for Experimental Biology
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