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Metabolomic analysis

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https://www.readbyqxmd.com/read/28534597/metabolomics-for-improving-pregnancy-outcomes-in-women-undergoing-assisted-reproductive-technologies
#1
REVIEW
Charalampos S Siristatidis, Eleni Sertedaki, Dennis Vaidakis
BACKGROUND: In order to overcome the low effectiveness of assisted reproductive technologies (ART) and the high incidence of multiple births, metabolomics is proposed as a non-invasive method to assess oocyte quality, embryo viability, and endometrial receptivity, and facilitate a targeted subfertility treatment. OBJECTIVES: To evaluate the effectiveness and safety of metabolomic assessment of oocyte quality, embryo viability, and endometrial receptivity for improving live birth or ongoing pregnancy rates in women undergoing ART, compared to conventional methods of assessment...
May 23, 2017: Cochrane Database of Systematic Reviews
https://www.readbyqxmd.com/read/28533028/optimizing-targeted-untargeted-metabolomics-by-automating-gas-chromatography-mass-spectrometry-gc-gc-ms-and-gc-ms-workflows
#2
Albert Robbat, Nicole Kfoury, Eugene Baydakov, Yuriy Gankin
New database building and MS subtraction algorithms have been developed for automated, sequential two-dimensional gas chromatography/mass spectrometry (GC-GC/MS). This paper reports the first use of a database building tool, with full mass spectrum subtraction, that does not rely on high resolution MS data. The software was used to automatically inspect GC-GC/MS data of high elevation tea from Yunnan, China, to build a database of 350 target compounds. The database was then used with spectral deconvolution to identify 285 compounds by GC/MS of the same tea...
May 8, 2017: Journal of Chromatography. A
https://www.readbyqxmd.com/read/28532626/single-nucleotide-polymorphisms-of-abcc2-modulate-renal-secretion-of-endogenous-organic-anions
#3
Kienana Muhrez, Bérenger Largeau, Patrick Emond, Montigny Frédéric, Jean-Michel Halimi, Patrick Trouillas, Chantal Barin-LE Guellec
The ATP-binding cassette family transporter MRP2 (multidrug resistance-associated protein 2), encoded by the ABCC2 gene, is involved in the renal excretion of numerous xenobiotics and it is likely that it also transports many endogenous molecules arising from not only normal essential metabolic processes but also from environmental toxins or food intake. We used a targeted gas chromatography-mass spectrometry metabolomics analysis to study whether endogenous organic anions are differentially excreted in urines of healthy volunteers according to their genotype for three functional single nucleotide polymorphisms (SNPs) in ABCC2...
May 19, 2017: Biochemical Pharmacology
https://www.readbyqxmd.com/read/28531831/workflow-methodology-for-rat-brain-metabolome-exploration-using-nmr-lc-ms-and-gc-ms-analytical-platforms
#4
Binta Diémé, Antoine Lefèvre, Lydie Nadal-Desbarats, Laurent Galineau, Blandine Madji Hounoum, Frédéric Montigny, Hélène Blasco, Christian R Andres, Patrick Emond, Sylvie Mavel
We developed a multi-platform approach for the metabolome exploration of rat brain tissue, using liquid chromatography coupled with mass spectrometry (LC-MS), nuclear magnetic resonance spectroscopy (NMR) and gas-chromatography coupled with mass spectrometry (GC-MS). The critical steps for metabolite exploration of cerebral tissues are tissue lysis and metabolites extraction. We first evaluated the impact of freeze-drying compared to wet tissue metabolites extraction using NMR and LC-MS with a reversed phase liquid chromatography...
May 13, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28530140/associations-of-nasopharyngeal-metabolome-and-microbiome-with-severity-among-infants-with-bronchiolitis-a-multi-omic-analysis
#5
Christopher J Stewart, Jonathan M Mansbach, Matthew C Wong, Nadim J Ajami, Joseph F Petrosino, Carlos A Camargo, Kohei Hasegawa
RATIONALE: Bronchiolitis is the most common lower respiratory infection in infants; however, it remains unclear which infants with bronchiolitis will develop severe illness. In addition, while emerging evidence indicates associations of the upper-airway microbiome with bronchiolitis severity, little is known about the mechanisms linking airway microbes and host response to disease severity. OBJECTIVES: To determine the relations among the nasopharyngeal airway metabolome profiles, microbiome profiles, and severity in infants with bronchiolitis...
May 21, 2017: American Journal of Respiratory and Critical Care Medicine
https://www.readbyqxmd.com/read/28529573/comparative-metabolomic-analysis-of-hpac-cells-following-the-acquisition-of-erlotinib-resistance
#6
Sooyeun Lee, Won-Jun Jang, Boyeon Choi, Sang Hoon Joo, Chul-Ho Jeong
Pancreatic cancer is one of the most lethal types of cancer, due to difficulty in early detection and the limited efficacy of available treatments. Erlotinib is used to inhibit the epidermal growth factor receptor for the treatment of pancreatic cancer; however, erlotinib resistance is a major issue and the mechanisms underlying the development of erlotinib resistance remain unclear. To better understand the alterations in tumor metabolism by acquired resistance to erlotinib, an erlotinib-resistant pancreatic cancer cell line (HPAC-ER) was established, followed by a comparison of the metabolic characteristics between these cells and their erlotinib-sensitive parental cells (HPAC)...
May 2017: Oncology Letters
https://www.readbyqxmd.com/read/28528542/performance-of-a-high-pressure-liquid-chromatography-ion-mobility-mass-spectrometry-system-for-metabolic-profiling
#7
Xing Zhang, Kimberly Kew, Richard Reisdorph, Mark Sartain, Roger Powell, Michael L Armstrong, Kevin Quinn, Charmion Cruickshank-Quinn, Scott Walmsley, Samantha S Bokatzian, Ed Darland, Matthew Rain, Kenneth Imatani, Nichole Reisdorph
A commercial liquid chromatography/drift tube ion mobility-mass spectrometer (LC/IM-MS) was evaluated for its utility in global metabolomics analysis. Performance was assessed using twelve targeted metabolite standards where the limit of detection (LOD), linear dynamic range, resolving power, and collision cross section (Ω), is reported for each standard. Data was collected in three different instrument operation modes: flow injection analysis with IM-MS (FIA/IM-MS), LC/MS and LC/IM-MS. Metabolomics analyses of human plasma and HaCaT cells were used to compare the above three operation modes...
May 22, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28528318/metabolic-profiling-of-goldfish-carassius-auratis-after-long-term-glyphosate-based-herbicide-exposure
#8
Ming-Hui Li, Ling-Yu Ruan, Jin-Wei Zhou, Yong-Hong Fu, Lei Jiang, He Zhao, Jun-Song Wang
Glyphosate is an efficient herbicide widely used worldwide. However, its toxicity to non-targeted organisms has not been fully elucidated. In this study, the toxicity of glyphosate-based herbicide was evaluated on goldfish (Carassius auratus) after long-term exposure. Tissues of brains, kidneys and livers were collected and submitted to NMR-based metabolomics analysis and histopathological inspection. Plasma was collected and the blood biochemical indexes of AST, ALT, BUN, CRE, LDH, SOD, GSH-Px, GR and MDA were measured...
May 13, 2017: Aquatic Toxicology
https://www.readbyqxmd.com/read/28527414/structural-characterization-and-discrimination-of-the-paris-polyphylla-var-yunnanensis-and-paris-vietnamensis-based-on-metabolite-profiling-analysis
#9
Li-Ping Kang, Yuan-Yuan Huang, Zhi-Lai Zhan, Da-Hui Liu, Hua-Sheng Peng, Tie-Gui Nan, Yuan Zhang, Qing-Xiu Hao, Jin-Fu Tang, Shou-Dong Zhu, Guang Yang, Lan-Ping Guo, Min Chen, Lu-Qi Huang
This study aimed to distinguish the rhizomes of Paris polyphylla var. yunnanensis (Franch) Hand Mazz (PPY) and Paris veitnamensis (Takht.) H. Li (PV) using metabolomics-based ultra high-performance liquid chromatography coupled with quadrupole time-of-fligh mass spectrometry (UHPLC/Q-TOF MS). First, the UHPLC/Q-TOF MS approach was optimized for metabolite profiling. Then, the MS data were processed using UNIFI™ combined with an in-house library to automatically characterize the metabolites. Based on the exact mass information, the fragmentation characteristics, and the retention time of compounds, and the fragmentation mechanism and retention behavior of steroidal glycosides in the references, the structures identified by UNIFI were further verified...
May 11, 2017: Journal of Pharmaceutical and Biomedical Analysis
https://www.readbyqxmd.com/read/28526818/essential-hypertension-a-filtered-serum-based-metabolomics-study
#10
Keerti Ameta, Ashish Gupta, Sudeep Kumar, Rishi Sethi, Deepak Kumar, Abbas Ali Mahdi
Despite the easy and reliable methods of blood pressure measurement, the screening of essential hypertension (EH) is usually ignored due to delayed onset of symptoms. A probe into the biochemical changes in hypertension would serve as a welcome asset to provide insight into the mechanistic aspects of EH. Filtered serum samples from 64 EH patients and 59 healthy controls (HC) were analysed using 800 MHz nuclear magnetic resonance (NMR) spectroscopy. Application of principal component analysis (PCA) and orthogonal partial least-squares discriminant analysis (OPLS-DA) following receiver operating characteristic (ROC) curve of NMR data reveals significantly perturbed metabolites: alanine, arginine, methionine, pyruvate, adenine, and uracil...
May 19, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28524099/metabolomics-of-therapy-response-in-preclinical-glioblastoma-a-multi-slice-mrsi-based-volumetric-analysis-for-noninvasive-assessment-of-temozolomide-treatment
#11
Nuria Arias-Ramos, Laura Ferrer-Font, Silvia Lope-Piedrafita, Victor Mocioiu, Margarida Julià-Sapé, Martí Pumarola, Carles Arús, Ana Paula Candiota
Glioblastoma (GBM) is the most common aggressive primary brain tumor in adults, with a short survival time even after aggressive therapy. Non-invasive surrogate biomarkers of therapy response may be relevant for improving patient survival. Previous work produced such biomarkers in preclinical GBM using semi-supervised source extraction and single-slice Magnetic Resonance Spectroscopic Imaging (MRSI). Nevertheless, GBMs are heterogeneous and single-slice studies could prevent obtaining relevant information. The purpose of this work was to evaluate whether a multi-slice MRSI approach, acquiring consecutive grids across the tumor, is feasible for preclinical models and may produce additional insight into therapy response...
May 18, 2017: Metabolites
https://www.readbyqxmd.com/read/28523725/differential-attenuation-of-nmr-signals-by-complementary-ion-exchange-resin-beads-for-de-novo-analysis-of-complex-metabolomics-mixtures
#12
Jiaqi Yuan, Bo Zhang, Rafael Bruschweiler
A primary goal of metabolomics is the characterization of a potentially very large number of metabolites that are part of complex mixtures. Application to biofluids and tissue samples offers insights into biochemical metabolic pathways and their role in health and disease. 1D 1H and 2D 13C-1H HSQC NMR spectra are most commonly used for this purpose. They yield quantitative information about each proton of the mixture, but not which protons belong to the same molecule. Interpretation requires the use of NMR spectral databases naturally limited to known metabolites...
May 18, 2017: Chemistry: a European Journal
https://www.readbyqxmd.com/read/28523497/maldi-msi-of-lipids-in-human-skin
#13
Philippa J Hart, Malcolm R Clench
Matrix-assisted laser desorption ionization (MALDI) mass spectrometry (MS) is now a well-established technique for imaging analysis of sectioned biological tissues. One of the growing areas of interest is in the analysis of skin. MALDI-MSI can provide a wealth of information from within sections of skin. This includes information on the distribution of pharmaceuticals following topical treatments, through to the examination of the composition of different skin layers and studies of proteomic, lipidomic, and metabolomic responses to disease, wounds, and external stimuli...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28521878/combining-a-nontargeted-and-targeted-metabolomics-approach-to-identify-metabolic-pathways-significantly-altered-in-polycystic-ovary-syndrome
#14
Alice Y Chang, Antigoni Z Lalia, Gregory D Jenkins, Tumpa Dutta, Rickey E Carter, Ravinder J Singh, K Sreekumaran Nair
OBJECTIVE: Polycystic ovary syndrome (PCOS) is a condition of androgen excess and chronic anovulation frequently associated with insulin resistance. We combined a nontargeted and targeted metabolomics approach to identify pathways and metabolites that distinguished PCOS from metabolic syndrome (MetS). METHODS: Twenty obese women with PCOS were compared with 18 obese women without PCOS. Both groups met criteria for MetS but could not have diabetes mellitus or take medications that treat PCOS or affect lipids or insulin sensitivity...
June 2017: Metabolism: Clinical and Experimental
https://www.readbyqxmd.com/read/28521615/comprehensive-evaluation-of-usnic-acid-induced-cardiotoxicity-in-rats-by-sequential-cross-omics-analysis
#15
Y Yokouchi, M Imaoka, N Niino, N Kiyosawa, K Kai
Two-week administration of (+)-usnic acid (UA) induces mitochondrial swelling of cardiomyocytes, and toxicogenomic analysis of the heart revealed upregulation of oxidative stress, amino acid limitation, and endoplasmic reticulum stress-related genes in rats. To analyze the pathogenesis, UA was orally administrated to rats for 1, 4, 7, and 14 days, and sequential histopathological, genomic, and metabolomic analyses were performed on the heart, liver, and plasma. As a result, mitochondrial swelling of cardiomyocytes was observed on day 15 preceded by genomic upregulation on days 5 and 8...
January 1, 2017: Toxicologic Pathology
https://www.readbyqxmd.com/read/28521388/non-targeted-high-resolution-mass-spectrometry-strategy-for-simultaneous-monitoring-of-xenobiotics-and-endogenous-compounds-in-green-sea-turtles-on-the-great-barrier-reef
#16
Amy L Heffernan, Maria M Gómez-Ramos, Caroline Gaus, Soumini Vijayasarathy, Ian Bell, Christine Hof, Jochen F Mueller, Maria J Gómez-Ramos
Chemical contamination poses a threat to ecosystem, biota and human health, and identifying these hazards is a complex challenge. Traditional hazard identification relies on a priori-defined targets of limited chemical scope, and is generally inappropriate for exploratory studies such as explaining toxicological effects in environmental systems. Here we present a non-target high resolution mass spectrometry environmental monitoring study with multivariate statistical analysis to simultaneously detect biomarkers of exposure (e...
May 14, 2017: Science of the Total Environment
https://www.readbyqxmd.com/read/28520899/increased-urinary-trimethylamine-n-oxide-tmao-following-cryptosporidium-infection-and-protein-malnutrition-independent-of-microbiome-effects
#17
D T Bolick, J Mayneris-Perxachs, G L Medlock, G L Kolling, J Papin, J R Swann, R L Guerrant
Cryptosporidium infections have been associated with growth stunting even in the absence of diarrhea. Having previously detailed the effects of protein deficiency on both microbiome and metabolome in this model, we now describe the specific gut microbial and biochemical effects of Cryptosporidium infection. Protein deficient mice were infected with Cryptosporidium parvum oocysts for 6-13 days and compared to uninfected controls. Following infection there was an increase in the urinary excretion of choline- and amino acid-derived metabolites...
May 17, 2017: Journal of Infectious Diseases
https://www.readbyqxmd.com/read/28520765/an-integrative-analysis-of-tissue-specific-transcriptomic-and-metabolomic-responses-to-short-term-dietary-methionine-restriction-in-mice
#18
Sujoy Ghosh, Laura A Forney, Desiree Wanders, Kirsten P Stone, Thomas W Gettys
Dietary methionine restriction (MR) produces a coordinated series of transcriptional responses in peripheral tissues that limit fat accretion, remodel lipid metabolism in liver and adipose tissue, and improve overall insulin sensitivity. Hepatic sensing of reduced methionine leads to induction and release of fibroblast growth factor 21 (FGF21), which acts centrally to increase sympathetic tone and activate thermogenesis in adipose tissue. FGF21 also has direct effects in adipose to enhance glucose uptake and oxidation...
2017: PloS One
https://www.readbyqxmd.com/read/28520403/integrated-strategy-for-unknown-ei-ms-identification-using-quality-control-calibration-curve-multivariate-analysis-ei-ms-spectral-database-and-retention-index-prediction
#19
Teruko Matsuo, Hiroshi Tsugawa, Hiromi Miyagawa, Eiichiro Fukusaki
Compound identification using unknown electron ionization (EI) mass spectra in gas chromatography coupled with mass spectrometry (GC-MS) is challenging in untargeted metabolomics, natural product chemistry, or exposome research. While the total count of EI-MS records included in publicly or commercially available databases is over 900,000, efficient use of this huge database has not been achieved in metabolomics. Therefore, we proposed a 'four-step' strategy for the identification of biologically significant metabolites using an integrated cheminformatics approach: (i) Quality control calibration curve to reduce background noise, (ii) variable selection by hypothesis testing in principal component analysis for the efficient selection of target peaks, (iii) searching the EI-MS spectral database, and (iv) retention index (RI) filtering in combination with RI predictions...
May 18, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28515731/ectopic-expression-of-cdf3-genes-in-tomato-enhances-biomass-production-and-yield-under-salinity-stress-conditions
#20
Begoña Renau-Morata, Rosa V Molina, Laura Carrillo, Jaime Cebolla-Cornejo, Manuel Sánchez-Perales, Stephan Pollmann, José Domínguez-Figueroa, Alba R Corrales, Jaume Flexas, Jesús Vicente-Carbajosa, Joaquín Medina, Sergio G Nebauer
Cycling Dof Factor (CDF) transcription factors (TFs) are involved in multiple processes related to plant growth and development. A member of this family, CDF3, has recently been linked in Arabidopsis to the regulation of primary metabolism and abiotic stress responses, but its role in crop production under stress is still unknown. In this study, we characterized tomato plants overexpressing the CDF3 genes from Arabidopsis and tomato and analyzed their effects on growth and yield under salinity, additionally gaining deeper insights into the molecular function of these TFs...
2017: Frontiers in Plant Science
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