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Metabolomic analysis

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https://www.readbyqxmd.com/read/28635678/evaluation-of-classifier-performance-for-multiclass-phenotype-discrimination-in-untargeted-metabolomics
#1
Patrick J Trainor, Andrew P DeFilippis, Shesh N Rai
Statistical classification is a critical component of utilizing metabolomics data for examining the molecular determinants of phenotypes. Despite this, a comprehensive and rigorous evaluation of the accuracy of classification techniques for phenotype discrimination given metabolomics data has not been conducted. We conducted such an evaluation using both simulated and real metabolomics datasets, comparing Partial Least Squares-Discriminant Analysis (PLS-DA), Sparse PLS-DA, Random Forests, Support Vector Machines (SVM), Artificial Neural Network, k-Nearest Neighbors (k-NN), and Naïve Bayes classification techniques for discrimination...
June 21, 2017: Metabolites
https://www.readbyqxmd.com/read/28634477/metabolomic-analysis-and-mode-of-action-of-metabolites-of-tea-tree-oil-involved-in-the-suppression-of-botrytis-cinerea
#2
Jiayu Xu, Xingfeng Shao, Yonghua Li, Yingying Wei, Feng Xu, Hongfei Wang
Tea tree oil (TTO), a volatile essential oil, has been widely used as an antimicrobial agent. However, the mechanism underlying TTO antifungal activity is not fully understood. In this study, a comprehensive metabolomics survey was undertaken to identify changes in metabolite production in Botrytis cinerea cells treated with TTO. Significant differences in 91 metabolites were observed, including 8 upregulated and 83 downregulated metabolites in TTO-treated cells. The results indicate that TTO inhibits primary metabolic pathways through the suppression of the tricarboxylic acid (TCA) cycle and fatty acid metabolism...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28632946/emerging-biomarkers-of-illness-severity-urinary-metabolites-associated-with-sepsis-and-necrotizing-methicillin-resistant-staphylococcus-aureus-pneumonia
#3
Lilliam Ambroggio, Todd A Florin, Samir S Shah, Richard Ruddy, Larisa Yeomans, Julie Trexel, Kathleen A Stringer
STUDY OBJECTIVE: To illustrate the potential of metabolomics to identify novel biomarkers of illness severity in a child with fatal necrotizing pneumonia caused by methicillin-resistant Staphylococcus aureus (MRSA). DESIGN: Case report with two control groups and a metabolomics analysis. PATIENTS: An infant with fatal MRSA pneumonia, four children with influenza pneumonia (pneumonia control group), and seven healthy children with no known infections (healthy control group)...
June 20, 2017: Pharmacotherapy
https://www.readbyqxmd.com/read/28630811/development-of-a-branched-radio-frequency-ion-trap-for-electron-based-dissociation-and-related-applications
#4
Takashi Baba, J Larry Campbell, J C Yves Le Blanc, Paul R S Baker, James W Hager, Bruce A Thomson
Collision-induced dissociation (CID) is the most common tool for molecular analysis in mass spectrometry to date. However, there are difficulties associated with many applications because CID does not provide sufficient information to permit details of the molecular structures to be elucidated, including post-translational-modifications in proteomics, as well as isomer differentiation in metabolomics and lipidomics. To face these challenges, we are developing fast electron-based dissociation devices using a novel radio-frequency ion trap (i...
2017: Mass Spectrometry
https://www.readbyqxmd.com/read/28629539/uplc-esi-qtof-ms-based-metabolomics-survey-on-the-toxicity-of-triptolide-and-detoxication-of-licorice
#5
Zhuo Wang, Jian-Qun Liu, Jin-Di Xu, He Zhu, Ming Kong, Guo-Hua Zhang, Su-Min Duan, Xiu-Yang Li, Guang-Fu Li, Li-Fang Liu, Song-Lin Li
Triptolide (TP) from Tripterygium wilfordii has been demonstrated to possess anti-inflammatory, immunosuppressive, and anticancer activities. TP is specially used for the treatment of awkward rheumatoid arthritis, but its clinical application is confined by intense side effects. It is reported that licorice can obviously reduce the toxicity of TP, but the detailed mechanisms involved have not been comprehensively investigated. The current study aimed to explore metabolomics characteristics of the toxic reaction induced by TP and the intervention effect of licorice water extraction (LWE) against such toxicity...
June 2017: Chinese Journal of Natural Medicines
https://www.readbyqxmd.com/read/28629310/editorial-identification-of-lead-compounds-using-metabolomic-analysis-in-drug-discovery
#6
EDITORIAL
Luciana Scotti, Marcus T Scotti, Ericsson Coy-Barrera
No abstract text is available yet for this article.
2017: Combinatorial Chemistry & High Throughput Screening
https://www.readbyqxmd.com/read/28629120/metabolomics-characterization-of-two-apocynaceae-plants-catharanthus-roseus-and-vinca-minor-using-gc-ms-and-lc-ms-methods-in-combination
#7
Qi Chen, Xueyan Lu, Xiaorui Guo, Qingxi Guo, Dewen Li
Catharanthus roseus (C. roseus) and Vinca minor (V. minor) are two common important medical plants belonging to the family Apocynaceae. In this study, we used non-targeted GC-MS and targeted LC-MS metabolomics to dissect the metabolic profile of two plants with comparable phenotypic and metabolic differences. A total of 58 significantly different metabolites were present in different quantities according to PCA and PLS-DA score plots of the GC-MS analysis. The 58 identified compounds comprised 16 sugars, eight amino acids, nine alcohols and 18 organic acids...
June 17, 2017: Molecules: a Journal of Synthetic Chemistry and Natural Product Chemistry
https://www.readbyqxmd.com/read/28628333/coupling-targeted-and-untargeted-mass-spectrometry-for-metabolome-microbiome-wide-association-studies-of-human-fecal-samples
#8
Alexey V Melnik, Pieter C Dorrestein, Ricardo R da Silva, Embriette R Hyde, Alexander A Aksenov, Fernando Vargas, Amina Bouslimani, Ivan Protsyuk, Alan Jarmusch, Anupriya Tripathi, Theodore Alexandrov, Rob Knight
Increasing appreciation of the gut microbiome's role in health motivates understanding the molecular composition of human feces. To analyze such complex samples, we developed a platform coupling targeted and untargeted metabolomics. The approach is facilitated through split flow from one UPLC, joint timing triggered by contact closure relays and a script to retrieve the data. It is designed to detect specific metabolites of interest with high sensitivity, allows for correction of targeted information, enables better quantitation thus providing an advanced analytical tool for exploratory studies...
June 19, 2017: Analytical Chemistry
https://www.readbyqxmd.com/read/28627685/metabolomic-analysis-based-on-1h-nuclear-magnetic-resonance-spectroscopy-metabolic-profiles-in-tuberculous-malignant-and-transudative-pleural-effusion
#9
Cheng Wang, Jingjin Peng, Yanling Kuang, Jiaqiang Zhang, Luming Dai
Pleural effusion is a common clinical manifestation with various causes. Current diagnostic and therapeutic methods have exhibited numerous limitations. By involving the analysis of dynamic changes in low molecular weight catabolites, metabolomics has been widely applied in various types of disease and have provided platforms to distinguish many novel biomarkers. However, to the best of our knowledge, there are few studies regarding the metabolic profiling for pleural effusion. In the current study, 58 pleural effusion samples were collected, among which 20 were malignant pleural effusions, 20 were tuberculous pleural effusions and 18 were transudative pleural effusions...
June 12, 2017: Molecular Medicine Reports
https://www.readbyqxmd.com/read/28627374/characterization-of-the-concurrent-metabolic-changes-in-brain-and-plasma-during-insulin-induced-moderate-hypoglycemia-using-1-h-nmr-spectroscopy-in-juvenile-rats
#10
Kathleen Ennis, Elizabeth Lusczek, Raghavendra Rao
Treatment of hypoglycemia in children is currently based on plasma glucose measurements. This approach may not ensure neuroprotection since plasma glucose does not reflect the dynamic state of cerebral energy metabolism. To determine whether cerebral metabolic changes during hypoglycemia could be better characterized using plasma metabolomic analysis, insulin-induced acute hypoglycemia was induced in 4-week-old rats. Brain tissue and concurrent plasma samples were collected from hypoglycemic (N=7) and control (N=7) rats after focused microwave fixation to prevent post-mortem metabolic changes...
June 14, 2017: Neuroscience Letters
https://www.readbyqxmd.com/read/28627174/integrative-analysis-of-renal-ischemia-reperfusion-injury-and-remote-ischemic-preconditioning-in-mice
#11
Kumsun Cho, Sang-Il Min, Sanghyun Ahn, Seung-Kee Min, Curie Ahn, Kyung-Sang Yu, In-Jin Jang, Joo-Youn Cho, Jongwon Ha
Remote ischemic preconditioning (RIPC) is a strategy to induce resistance in a target organ against the oxidative stress and injury caused by ischemia and reperfusion (IR). RIPC harnesses the body's endogenous protective capabilities through brief episodes of IR applied in organs remote from the target. Few studies have analyzed this phenomenon in the kidney. Furthermore, the window of protection representing RIPC efficacy has not been fully elucidated. Here, we performed a multi-omics study to specify those associated with protective effects of RIPC against the IR injury...
June 19, 2017: Journal of Proteome Research
https://www.readbyqxmd.com/read/28626765/serum-metabolomics-profiling-to-identify-biomarkers-for-unstable-angina
#12
Wei Yao, Yuxia Gao, Zheng Wan
Although statistical evidence is clear regarding the dangerousness of unstable angina (UA), a form of coronary heart disease (CHD) characterised by high mortality and morbidity globally, it is important to recognise that diagnostic precision for the condition is unfavourable. In the present research, to gain insight into candidate biomarkers, the author draws on (1)H NMR-based serum metabolic profiling to analyze the unstable angina pectoris (UAP) metabolic signatures; this constitutes an effective way to produce medical diagnosis...
2017: BioMed Research International
https://www.readbyqxmd.com/read/28626361/molecular-biomarkers-of-colorectal-cancer-and-cancer-disparities-current-status-and-perspective
#13
Upender Manne, Trafina Jadhav, Balananda-Dhurjati Kumar Putcha, Temesgen Samuel, Shivani Soni, Chandrakumar Shanmugam, Esther A Suswam
This review provides updates on the efforts for the development of prognostic and predictive markers in colorectal cancer based on the race/ethnicity of patients. Since the clinical consequences of genetic and molecular alterations differ with patient race and ethnicity, the usefulness of these molecular alterations as biomarkers needs to be evaluated in different racial/ethnic groups. To accomplish personalized patient care, a combined analysis of multiple molecular alterations in DNA, RNA, microRNAs (miRNAs), metabolites, and proteins in a single test is required to assess disease status in a precise way...
December 2016: Current Colorectal Cancer Reports
https://www.readbyqxmd.com/read/28625405/metabolomic-analysis-with-1-h-nmr-for-non-invasive-diagnosis-of-hepatic-fibrosis-degree-in-patients-with-chronic-hepatitis-c
#14
Tommaso Gabbani, Maria Marsico, Patrizia Bernini, Elisabetta Lorefice, Cecilia Grappone, Maria Rosa Biagini, Stefano Milani, Vito Annese
BACKGROUND: The assessment of fibrosis degree in liver diseases is based on several non-invasive techniques, but none has been accurate. AIM: This study employed proton nuclear magnetic resonance spectroscopy to identify metabolic profiles in serum and urine, specific for different fibrosis degree in chronic hepatitis C patients. METHOD: 71 plasma, 73 serum, and 578 urine samples were collected. All samples were analyzed using (1)H-NMR spectroscopy technique and three different NMR spectra were acquired for each serum/plasma sample...
June 13, 2017: Digestive and Liver Disease
https://www.readbyqxmd.com/read/28625351/challenges-of-non-flocculating-saccharomyces-cerevisiae-haploid-strain-against-inhibitory-chemical-complex-for-ethanol-production
#15
Prihardi Kahar, Eny Ida Riyanti, Hiromi Otsuka, Hana Matsumoto, Chie Kihira, Chiaki Ogino, Akihiko Kondo
This study provides insight observation based on the gene expression and the metabolomic analysis of the natural robust yeast Saccharomyces cerevisiae NBRC849 during the fermentation in the medium containing inhibitory chemical complexes (ICC) at different concentrations. The tolerance mechanisms involved in the strain might have existed through the upregulation of genes involved in NAD(H)/NADP(H) cofactors generations (ALD6, ZWF1, GND1), membrane robustness for efflux pump (YOR1, PDR5, TPO3) and cation/polyamine transport (TPO3)...
June 15, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28624903/early-diagnosis-of-sepsis-is-an-integrated-omics-approach-the-way-forward
#16
REVIEW
Raymond J Langley, Hector R Wong
Sepsis remains one of the leading causes of death in the USA and it is expected to get worse as the population ages. Moreover, the standard of care, which recommends aggressive treatment with appropriate antibiotics, has led to an increase in multiple drug-resistant organisms. There is a dire need for the development of new antibiotics, improved antibiotic stewardship, and therapies that treat the host response. Development of new sepsis therapeutics has been a disappointment as no drugs are currently approved to treat the various complications from sepsis...
June 17, 2017: Molecular Diagnosis & Therapy
https://www.readbyqxmd.com/read/28624380/plasma-phospholipids-and-sphingolipids-identify-stent-restenosis-after-percutaneous-coronary-intervention
#17
Song Cui, Kefeng Li, Lawrence Ang, Jinghua Liu, Liqian Cui, Xiantao Song, Shuzheng Lv, Ehtisham Mahmud
OBJECTIVES: The aim of this study was to evaluate the diagnostic utility of plasma metabolomic biomarkers for in-stent restenosis (ISR). BACKGROUND: ISR remains an issue for patients after percutaneous coronary intervention. Identification of biomarkers to predict ISR could be invaluable for patient care. METHODS: Next-generation metabolomic profiling was performed in the discovery phase from the plasma of 400 patients undergoing percutaneous coronary intervention...
June 7, 2017: JACC. Cardiovascular Interventions
https://www.readbyqxmd.com/read/28622800/analysis-of-stable-isotope-assisted-metabolomics-data-acquired-by-gc-ms
#18
Xiaoli Wei, Biyun Shi, Imhoi Koo, Xinmin Yin, Pawel Lorkiewicz, Hamid Suhail, Ramandeep Rattan, Shailendra Giri, Craig J McClain, Xiang Zhang
Stable isotope assisted metabolomics (SIAM) measures the abundance levels of metabolites in a particular pathway using stable isotope tracers (e.g., (13)C, (18)O and/or (15)N). We report a method termed signature ion approach for analysis of SIAM data acquired on a GC-MS system equipped with an electron ionization (EI) ion source. The signature ion is a fragment ion in EI mass spectrum of a derivatized metabolite that contains all atoms of the underivatized metabolite, except the hydrogen atoms lost during derivatization...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28622799/quantitative-nmr-analysis-of-intra-and-extracellular-metabolism-of-mammalian-cells-a-tutorial
#19
REVIEW
Sarantos Kostidis, Ruben D Addie, Hans Morreau, Oleg A Mayboroda, Martin Giera
Metabolomics analysis of body fluids as well as cells is depended on many factors. While several well-accepted standard operating procedures for the analysis of body fluids are available, the NMR based quantitative analysis of cellular metabolites is less well standardized. Experimental designs depend on the cell type, the quenching protocol and the applied post-acquisition workflow. Here, we provide a tutorial for the quantitative description of the metabolic phenotype of mammalian cells using NMR spectroscopy...
August 8, 2017: Analytica Chimica Acta
https://www.readbyqxmd.com/read/28622688/integration-of-metabolomics-transcriptomics-and-microrna-expression-profiling-reveals-a-mir-143-hk2-glucose-network-underlying-zinc-deficiency-associated-esophageal-neoplasia
#20
Louise Y Fong, Ruiyan Jing, Karl J Smalley, Cristian Taccioli, Johannes Fahrmann, Dinesh K Barupal, Hansjuerg Alder, John L Farber, Oliver Fiehn, Carlo M Croce
Esophageal squamous cell carcinoma (ESCC) in humans is a deadly disease associated with dietary zinc (Zn)-deficiency. In the rat esophagus, Zn-deficiency induces cell proliferation, alters mRNA and microRNA gene expression, and promotes ESCC. We investigated whether Zn-deficiency alters cell metabolism by evaluating metabolomic profiles of esophageal epithelia from Zn-deficient and replenished rats vs sufficient rats, using untargeted gas chromatography time-of-flight mass spectrometry (n = 8/group). The Zn-deficient proliferative esophagus exhibits a distinct metabolic profile with glucose down 153-fold and lactic acid up 1...
June 9, 2017: Oncotarget
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