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"Untargeted metabolomics"

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https://www.readbyqxmd.com/read/29674491/ketamine-pharmacokinetics-and-pharmacodynamics-are-altered-by-pgp-and-bcrp-efflux-transporters-in-mice
#1
Samit Ganguly, John C Panetta, Jessica K Roberts, Erin G Schuetz
To understand the systemic impact of Bcrp and Pgp deletion, untargeted metabolomics was performed on CSF and plasma of wild-type (WT) and Pgp and Bcrp double knockout (dKO) rats anesthetized with ketamine-xylazine. We unexpectedly found elevated ketamine levels in both CSF and plasma of dKO versus WT rats. Therefore, the effect of these transporters was investigated on ketamine's (i) oral (PO) and intraperitoneal (IP) serum pharmacokinetics (PK), using a liquid chromatography (HPLC-UV) method, and (ii) anesthetic effect using a duration of loss of righting reflex (dLORR) test in WT, Bcrp KO, Pgp KO, and Pgp-Bcrp dKO mice...
April 19, 2018: Drug Metabolism and Disposition: the Biological Fate of Chemicals
https://www.readbyqxmd.com/read/29671321/a-comparative-metabolomics-approach-detects-stress-specific-responses-during-coral-bleaching-in-soft-corals
#2
Mohamed A Farag, Achim Meyer, Sara E Ali, Mohamed A Salem, Patrick Giavalisco, Hildegard Westphal, Ludger A Wessjohann
Chronic exposure to ocean acidification and elevated sea-surface temperatures pose significant stress to marine ecosystems. This in turn necessitates costly acclimation responses in corals in both the symbiont and host, with a re-organization of cell metabolism and structure. A large-scale untargeted metabolomics approach comprising gas chromatography mass spectrometry (GC-MS) and ultra performance liquid chromatography coupled to high resolution mass spectrometry (UPLC-MS) was applied to profile the metabolite composition of the soft coral Sarcophyton ehrenbergi and its dinoflagellate symbiont...
April 19, 2018: Journal of Proteome Research
https://www.readbyqxmd.com/read/29670016/recent-advances-in-targeted-and-untargeted-metabolomics-by-nmr-and-ms-nmr-methods
#3
REVIEW
Kerem Bingol
Metabolomics has made significant progress in multiple fronts in the last 18 months. This minireview aimed to give an overview of these advancements in the light of their contribution to targeted and untargeted metabolomics. New computational approaches have emerged to overcome the manual absolute quantitation step of metabolites in one-dimensional (1D) ¹H nuclear magnetic resonance (NMR) spectra. This provides more consistency between inter-laboratory comparisons. Integration of two-dimensional (2D) NMR metabolomics databases under a unified web server allowed for very accurate identification of the metabolites that have been catalogued in these databases...
April 18, 2018: High-throughput
https://www.readbyqxmd.com/read/29669882/influential-parameters-for-the-analysis-of-intracellular-parasite-metabolomics
#4
Maureen A Carey, Vincent Covelli, Audrey Brown, Gregory L Medlock, Mareike Haaren, Jessica G Cooper, Jason A Papin, Jennifer L Guler
Metabolomics is increasingly popular for the study of pathogens. For the malaria parasite Plasmodium falciparum , both targeted and untargeted metabolomics have improved our understanding of pathogenesis, host-parasite interactions, and antimalarial drug treatment and resistance. However, purification and analysis procedures for performing metabolomics on intracellular pathogens have not been explored. Here, we purified in vitro -grown ring-stage intraerythrocytic P. falciparum parasites for untargeted metabolomics studies; the small size of this developmental stage amplifies the challenges associated with metabolomics studies as the ratio between host and parasite biomass is maximized...
April 25, 2018: MSphere
https://www.readbyqxmd.com/read/29660695/metabolite-profiles-of-striped-marsh-frog-limnodynastes-peronii-larvae-exposed-to-the-anti-androgenic-fungicides-vinclozolin-and-propiconazole-are-consistent-with-altered-steroidogenesis-and-oxidative-stress
#5
Steven D Melvin, Frederic D L Leusch, Anthony R Carroll
Amphibians use wetlands in urban and agricultural landscapes for breeding, growth and development. Fungicides and other pesticides used in these areas have therefore been identified as potential threats that could contribute towards amphibian population declines. However, relatively little is known about how such chemicals influence sensitive early life-stages or how short episodic exposures influence sub-lethal physiological and metabolic pathways. The present study applied untargeted metabolomics to evaluate effects in early post-hatch amphibian larvae exposed to the anti-androgenic fungicides vinclozolin and propiconazole...
April 11, 2018: Aquatic Toxicology
https://www.readbyqxmd.com/read/29651531/effects-of-glaucocalyxin-a-on-human-liver-cancer-cells-as-revealed-by-gc-ms-and-lc-ms-based-metabolic-profiling
#6
Yue Liu, Shan Lu, Liang Zhao, Xin Dong, Zhenyu Zhu, Yongsheng Jin, Haisheng Chen, Feng Lu, Zhanying Hong, Yifeng Chai
Studies have documented the potential antitumor activities of glaucocalyxin A (GLA), an ent-kaurene diterpenoid isolated from Rabdosia japonica. However, the metabolic mechanism underlying the antitumor activity of GLA remains largely unknown. The effects of GLA on the metabolome of human liver cancer cells using GC/MS- and LC/MS-based metabolic profiling have been investigated. An untargeted metabolomics approach in conjunction with orthogonal projection to latent structures-discriminant analysis (OPLS-DA) has been developed to characterize the metabolic modifications induced by GLA treatment in human hepatoma cell line SMMC7721...
April 13, 2018: Analytical and Bioanalytical Chemistry
https://www.readbyqxmd.com/read/29642378/pasture-feeding-changes-the-bovine-rumen-and-milk-metabolome
#7
Tom F O'Callaghan, Rosa Vázquez-Fresno, Arnau Serra-Cayuela, Edison Dong, Rupasri Mandal, Deirdre Hennessy, Stephen McAuliffe, Pat Dillon, David S Wishart, Catherine Stanton, R Paul Ross
The purpose of this study was to examine the effects of two pasture feeding systems-perennial ryegrass (GRS) and perennial ryegrass and white clover (CLV)-and an indoor total mixed ration (TMR) system on the (a) rumen microbiome; (b) rumen fluid and milk metabolome; and (c) to assess the potential to distinguish milk from different feeding systems by their respective metabolomes. Rumen fluid was collected from nine rumen cannulated cows under the different feeding systems in early, mid and late lactation, and raw milk samples were collected from ten non-cannulated cows in mid-lactation from each of the feeding systems...
April 6, 2018: Metabolites
https://www.readbyqxmd.com/read/29609095/a-comparative-proteomic-characterization-and-nutritional-assessment-of-naturally-and-artificially-cultivated-cordyceps-sinensis
#8
Xu Zhang, Qun Liu, Wei Zhou, Ping Li, Raphael N Alolga, Zhenming Qian, Wenjia Li, Lian-Wen Qi, Xiaojian Yin
Cordyceps sinensis has gained increasing attention due to its nutritional and medicinal properties. Herein, we employed label-free quantitative mass spectrometry to explore the proteome differences between naturally- and artificially-cultivated C. sinensis. A total of 22,829 peptides with confidence ≥95%, corresponding to 2541 protein groups were identified from the caterpillar bodies/stromata of 12 naturally- and artificially-cultivated samples of C. sinensis. Among them, 341 proteins showed significant differences between the samples of natural and artificial cultivation...
March 30, 2018: Journal of Proteomics
https://www.readbyqxmd.com/read/29606928/bayesian-estimation-of-the-number-of-protonation-sites-for-urinary-metabolites-from-nmr-spectroscopic-data
#9
Lifeng Ye, Maria De Iorio, Timothy M D Ebbels
Introduction: To aid the development of better algorithms for [Formula: see text]H NMR data analysis, such as alignment or peak-fitting, it is important to characterise and model chemical shift changes caused by variation in pH. The number of protonation sites, a key parameter in the theoretical relationship between pH and chemical shift, is traditionally estimated from the molecular structure, which is often unknown in untargeted metabolomics applications. Objective: We aim to use observed NMR chemical shift titration data to estimate the number of protonation sites for a range of urinary metabolites...
2018: Metabolomics: Official Journal of the Metabolomic Society
https://www.readbyqxmd.com/read/29599484/prophylactic-ketamine-alters-nucleotide-and-neurotransmitter-metabolism-in-brain-and-plasma-following-stress
#10
Josephine C McGowan, Collin Hill, Alessia Mastrodonato, Christina T LaGamma, Alexander Kitayev, Rebecca A Brachman, Niven R Narain, Michael A Kiebish, Christine A Denny
Recently, we have shown that ketamine given prior to stress exposure protects against the development of depressive-like behavior in mice. These data suggest that it may be possible to prevent the induction of affective disorders before they develop by administering prophylactic pharmaceuticals, a relatively nascent and unexplored strategy for psychiatry. Here, we performed metabolomics analysis of brain and plasma following prophylactic ketamine treatment in order to identify markers of stress resilience enhancement...
March 29, 2018: Neuropsychopharmacology: Official Publication of the American College of Neuropsychopharmacology
https://www.readbyqxmd.com/read/29593653/identification-of-metabolomic-biomarkers-for-endometrial-cancer-and-its-recurrence-after-surgery-in-postmenopausal-women
#11
Yannick Audet-Delage, Lyne Villeneuve, Jean Grégoire, Marie Plante, Chantal Guillemette
Endometrial cancer (EC) is the most frequent gynecological cancer in developed countries. Most EC occurs after menopause and is diagnosed as endometrioid (type I) carcinomas, which exhibit a favorable prognosis. In contrast, non-endometrioid (type II) carcinomas such as serous tumors have a poor prognosis. Our goal was to identify novel blood-based markers associated with EC subtypes and recurrence after surgery in postmenopausal women. Using mass spectrometry-based untargeted metabolomics, we examined preoperative serum metabolites among control women ( n  = 18) and those with non-recurrent (NR) and recurrent (R) cases of type I endometrioid ( n  = 24) and type II serous ( n  = 12) carcinomas...
2018: Frontiers in Endocrinology
https://www.readbyqxmd.com/read/29581584/biosynthesis-of-redox-active-metabolites-in-response-to-iron-deficiency-in-plants
#12
Jakub Rajniak, Ricardo F H Giehl, Evelyn Chang, Irene Murgia, Nicolaus von Wirén, Elizabeth S Sattely
Iron is an essential but poorly bioavailable nutrient because of its low solubility, especially in alkaline soils. Here, we describe the discovery of a previously undescribed redox-active catecholic metabolite, termed sideretin, which derives from the coumarin fraxetin and is the primary molecule exuded by Arabidopsis thaliana roots in response to iron deficiency. We identified two enzymes that complete the biosynthetic pathway of fraxetin and sideretin. Chemical characterization of fraxetin and sideretin, and biological assays with pathway mutants, suggest that these coumarins are critical for iron nutrition in A...
May 2018: Nature Chemical Biology
https://www.readbyqxmd.com/read/29579910/effect-of-dietary-fiber-inulin-addition-on-phenolics-and-in-vitro-bioaccessibility-of-tomato-sauce
#13
Merve Tomas, Jules Beekwilder, Robert D Hall, Carmen Diez Simon, Osman Sagdic, Esra Capanoglu
The effect of the addition of inulin (5 and 10%) on the phenolic content and in vitro gastrointestinal digestion of tomato sauces has been investigated. Results have shown that the addition of inulin to tomato sauce significantly decreased the total phenolic content (57-68%), total flavonoid content (48-60%), and total antioxidant capacity (49-61%). Similarly, all assays of the sauce containing both 5% and 10% inulin, showed a slight decrease during in vitro gastrointestinal digestion of tomato sauces. Higher levels of inulin added to tomato sauce resulted in the greatest decrease in phenolic content, probably because of the interaction between inulin and phenolic compounds...
April 2018: Food Research International
https://www.readbyqxmd.com/read/29578100/wisdom-of-artificial-crowds-feature-selection-in-untargeted-metabolomics-an-application-to-the-development-of-a-blood-based-diagnostic-test-for-thrombotic-myocardial-infarction
#14
Patrick J Trainor, Roman V Yampolskiy, Andrew P DeFilippis
INTRODUCTION: Heart disease remains a leading cause of global mortality. While acute myocardial infarction (colloquially: heart attack), has multiple proximate causes, proximate etiology cannot be determined by a blood-based diagnostic test. We enrolled a suitable patient cohort and conducted a non-targeted quantification of plasma metabolites by mass spectrometry for developing a test that can differentiate between thrombotic MI, non-thrombotic MI, and stable disease. A significant challenge in developing such a diagnostic test is solving the NP-hard problem of feature selection for constructing an optimal statistical classifier...
March 22, 2018: Journal of Biomedical Informatics
https://www.readbyqxmd.com/read/29572891/novel-link-between-gut-microbiome-derived-metabolite-and-shared-gene-effects-with-hepatic-steatosis-and-fibrosis-in-nafld
#15
Cyrielle Caussy, Cynthia Hsu, Min-Tzu Lo, Amy Liu, Ricki Bettencourt, Veeral H Ajmera, Shirin Bassirian, Jonathan Hooker, Ethan Sy, Lisa Richards, Nicholas Schork, Bernd Schnabl, David A Brenner, Claude B Sirlin, Chi-Hua Chen, Rohit Loomba
Previous studies have shown that gut-microbiome is associated with nonalcoholic fatty liver disease (NAFLD). We aimed to examine if serum metabolites especially those derived from the gut-microbiome have a shared gene-effect with hepatic steatosis and fibrosis. This is a cross-sectional analysis of a prospective discovery cohort including 156 well-characterized Twins and Families with untargeted metabolome profiling assessment. Hepatic steatosis was assessed using magnetic-resonance-imaging proton-density-fat-fraction (MRI-PDFF) and fibrosis using MR-elastography (MRE)...
March 23, 2018: Hepatology: Official Journal of the American Association for the Study of Liver Diseases
https://www.readbyqxmd.com/read/29572459/untargeted-metabolomics-reveals-a-new-mode-of-action-of-pretomanid-pa-824
#16
Rafael Baptista, David M Fazakerley, Manfred Beckmann, Les Baillie, Luis A J Mur
Pretomanid is a promising anti-tubercular drug currently at clinical phase III, but its mechanisms of action are currently unclear. This study aimed to: (i) reveal the metabolome of Mycobacterium smegmatis under pretomanid treatment; (ii) compare major sources of metabolite variation in bacteria treated with pretomanid treatment and other antibiotics; and (iii) to target metabolites responsible for the killing activity of pretomanid in mycobacteria. Untargeted high-resolution metabolite profiling was carried out using flow infusion electrospray ion high resolution mass spectrometry (FIE-HRMS) to identify and quantify metabolites...
March 23, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29571150/metabolomic-analysis-applied-to-chemosystematics-and-evolution-of-megadiverse-brazilian-vernonieae-asteraceae
#17
Marília Elias Gallon, Marcelo Monge, Rosana Casoti, Fernando Batista Da Costa, João Semir, Leonardo Gobbo-Neto
Vernonia sensu lato is the largest and most complex genus of the tribe Vernonieae (Asteraceae). The tribe is chemically characterized by the presence of sesquiterpene lactones and flavonoids. Over the years, several taxonomic classifications have been proposed for Vernonia s.l. and for the tribe; however, there has been no consensus among the researches. According to traditional classification, Vernonia s.l. comprises more than 1000 species divided into sections, subsections and series (sensu Bentham). In a more recent classification, these species have been segregated into other genera and some subtribes were proposed, while the genus Vernonia sensu stricto was restricted to 22 species distributed mainly in North America (sensu Robinson)...
March 20, 2018: Phytochemistry
https://www.readbyqxmd.com/read/29571133/lc-ms-based-serum-fingerprinting-reveals-significant-dysregulation-of-phospholipids-in-chronic-heart-failure
#18
M Marcinkiewicz-Siemion, M Ciborowski, K Ptaszynska-Kopczynska, A Szpakowicz, A Lisowska, M Jasiewicz, E Waszkiewicz, A Kretowski, W J Musial, K A Kaminski
Cardiac and extracardiac lipid metabolism is known to be significantly altered in the course of the heart failure with reduced ejection fraction (HF-REF), however the precise mechanisms are not fully elucidated. The aim of the study was to use of untargeted metabolomics to identify and validate changes in the blood metabolites profile, occurring as a result of HF-REF development. The analyses were performed first in the derivation set (36 chronic HF-REF patients and 19 controls without the disease) and repeated in validation cohort (31 chronic HF-REF patients and 20 controls)...
March 15, 2018: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/29567248/the-integration-of-multi-platform-ms-based-metabolomics-and-multivariate-analysis-for-the-geographical-origin-discrimination-of-oryza-sativa-l
#19
Dong Kyu Lim, Changyeun Mo, Jeong Hee Lee, Nguyen Phuoc Long, Ziyuan Dong, Jing Li, Jongguk Lim, Sung Won Kwon
For the authentication of white rice from different geographical origins, the selection of outstanding discrimination markers is essential. In this study, 80 commercial white rice samples were collected from local markets of Korea and China and discriminated by mass spectrometry-based untargeted metabolomics approaches. Additionally, the potential markers that belong to sugars & sugar alcohols, fatty acids, and phospholipids were examined using several multivariate analyses to measure their discrimination efficiencies...
April 2018: Journal of Food and Drug Analysis
https://www.readbyqxmd.com/read/29563342/untargeted-metabolomics-identifies-trimethyllysine-a-tmao-producing-nutrient-precursor-as-a-predictor-of-incident-cardiovascular-disease-risk
#20
Xinmin S Li, Zeneng Wang, Tomas Cajka, Jennifer A Buffa, Ina Nemet, Alex G Hurd, Xiaodong Gu, Sarah M Skye, Adam B Roberts, Yuping Wu, Lin Li, Christopher J Shahen, Matthew A Wagner, Jaana A Hartiala, Robert L Kerby, Kymberleigh A Romano, Yi Han, Slayman Obeid, Thomas F Lüscher, Hooman Allayee, Federico E Rey, Joseph A DiDonato, Oliver Fiehn, W H Wilson Tang, Stanley L Hazen
Using an untargeted metabolomics approach in initial (N = 99 subjects) and replication cohorts (N = 1,162), we discovered and structurally identified a plasma metabolite associated with cardiovascular disease (CVD) risks, N6,N6,N6-trimethyl-L-lysine (trimethyllysine, TML). Stable-isotope-dilution tandem mass spectrometry analyses of an independent validation cohort (N = 2,140) confirmed TML levels are independently associated with incident (3-year) major adverse cardiovascular event risks (hazards ratio [HR], 2...
March 22, 2018: JCI Insight
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