Integrative Molecular Phenotyping
INTEGRATIVE MOLECULAR
PHENOTYPING
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY
DEPARTMENT OF MEDICAL
BIOCHEMISTRY AND BIOPHYSICS
WHEELOCK LABORATORY

PubMed

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PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 5 min 44 sec ago

Gut microbiota and plasma metabolites associated with diabetes in women with, or at high risk for, HIV infection.

Sun, 28/10/2018 - 13:19
Related Articles Gut microbiota and plasma metabolites associated with diabetes in women with, or at high risk for, HIV infection. EBioMedicine. 2018 Oct 23;: Authors: Moon JY, Zolnik CP, Wang Z, Qiu Y, Usyk M, Wang T, Kizer JR, Landay AL, Kurland IJ, Anastos K, Kaplan RC, Burk RD, Qi Q Abstract BACKGROUND: Gut microbiota alteration has been implicated in HIV infection and metabolic disorders. The relationship between gut microbiota and diabetes has rarely been studied in HIV-infected individuals, who have excess risk of metabolic disorders. METHODS: Our study during 2015-2016 enrolled predominantly African Americans and Hispanics in the Women's Interagency HIV Study. We studied 28 women with long-standing HIV infection under antiretroviral therapy and 20 HIV-uninfected, but at high risk of infection, women (16 HIV+ and 6 HIV- with diabetes). Fecal samples were analyzed by sequencing prokaryotic16S rRNA gene. Plasma metabolomics profiling was performed by liquid chromatography-tandem mass spectrometry. FINDINGS: No significant differences in bacterial α- or β-diversity were observed by diabetes or HIV serostatus (all P > .1). Relative abundances of four genera (Finegoldia, Anaerococcus, Sneathia, and Adlercreutzia) were lower in women with diabetes compared to those without diabetes (all P < .01). In women with diabetes, plasma levels of several metabolites in tryptophan catabolism (e,g., kynurenine/tryptophan ratio), branched-chain amino acid and proline metabolism pathways were higher, while glycerophospholipids were lower (all P < .05). Results were generally consistent between HIV-infected and HIV-uninfected women, and no significant modification effects by HIV serostatus were observed (all Pinteraction > 0.05). Anaerococcus, known to produce butyrate which is involved in anti-inflammation and glucose metabolism, showed an inverse correlation with kynurenine/tryptophan ratio (r = -0.38, P < .01). INTERPRETATION: Among women with or at high risk for HIV infection, diabetes is associated with gut microbiota and plasma metabolite alteration, including depletion of butyrate-producing bacterial population along with higher tryptophan catabolism. FUND: NHLBI (K01HL129892, R01HL140976) and FMF. PMID: 30366816 [PubMed - as supplied by publisher]

Microbial Sterolomics as a Chemical Biology Tool.

Sun, 28/10/2018 - 13:19
Related Articles Microbial Sterolomics as a Chemical Biology Tool. Molecules. 2018 Oct 25;23(11): Authors: Haubrich BA Abstract Metabolomics has become a powerful tool in chemical biology. Profiling the human sterolome has resulted in the discovery of noncanonical sterols, including oxysterols and meiosis-activating sterols. They are important to immune responses and development, and have been reviewed extensively. The triterpenoid metabolite fusidic acid has developed clinical relevance, and many steroidal metabolites from microbial sources possess varying bioactivities. Beyond the prospect of pharmacognostical agents, the profiling of minor metabolites can provide insight into an organism's biosynthesis and phylogeny, as well as inform drug discovery about infectious diseases. This review aims to highlight recent discoveries from detailed sterolomic profiling in microorganisms and their phylogenic and pharmacological implications. PMID: 30366429 [PubMed - in process]

Excavatolide-B Enhances Contextual Memory Retrieval via Repressing the Delayed Rectifier Potassium Current in the Hippocampus.

Sun, 28/10/2018 - 13:19
Related Articles Excavatolide-B Enhances Contextual Memory Retrieval via Repressing the Delayed Rectifier Potassium Current in the Hippocampus. Mar Drugs. 2018 Oct 25;16(11): Authors: Huang IY, Hsu YL, Chen CC, Chen MF, Wen ZH, Huang HT, Liu IY Abstract Memory retrieval dysfunction is a symptom of schizophrenia, autism spectrum disorder (ASD), and absence epilepsy (AE), as well as an early sign of Alzheimer's disease. To date, few drugs have been reported to enhance memory retrieval. Here, we found that a coral-derived natural product, excavatolide-B (Exc-B), enhances contextual memory retrieval in both wild-type and Cav3.2-/- mice via repressing the delayed rectifier potassium current, thus lowering the threshold for action potential initiation and enhancing induction of long-term potentiation (LTP). The human CACNA1H gene encodes a T-type calcium channel (Cav3.2), and its mutation is associated with schizophrenia, ASD, and AE, which are all characterized by abnormal memory function. Our previous publication demonstrated that Cav3.2-/- mice exhibit impaired contextual-associated memory retrieval, whilst their retrieval of spatial memory and auditory cued memory remain intact. The effect of Exc-B on enhancing the retrieval of context-associated memory provides a hope for novel drug development. PMID: 30366389 [PubMed - in process]

metabolomics; +23 new citations

Sat, 27/10/2018 - 14:01
23 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/27PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +40 new citations

Fri, 26/10/2018 - 16:29
40 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/26PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +40 new citations

Fri, 26/10/2018 - 13:29
40 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/26PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +22 new citations

Wed, 24/10/2018 - 15:36
22 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/24PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +22 new citations

Wed, 24/10/2018 - 12:35
22 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/24PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +20 new citations

Tue, 23/10/2018 - 15:12
20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/23PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

metabolomics; +20 new citations

Tue, 23/10/2018 - 12:10
20 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/23PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

A novel strategy for rapid screening of the complex triterpene saponin mixture present in the methanolic extract of blackberry leaves (Rubus cv. Loch Ness) by UHPLC/QTOF-MS.

Mon, 22/10/2018 - 14:56
Related Articles A novel strategy for rapid screening of the complex triterpene saponin mixture present in the methanolic extract of blackberry leaves (Rubus cv. Loch Ness) by UHPLC/QTOF-MS. J Pharm Biomed Anal. 2018 Oct 07;164:47-56 Authors: Gradillas A, Martínez-Alcázar MP, Gutiérrez E, Ramos-Solano B, García A Abstract Triterpene saponins are important chemical constituents in blackberry leaves and have significant antimicrobial activity, among other healthful properties. In this study, a new UHPLC-MS method was optimized with outstanding efficiency for a non-targeted metabolic approach and comprehensive analysis of bioactive compounds in blackberry leaves (Rubus cv. Loch Ness). With minimum sample treatment, phenols and triterpene saponins, among others, were separated according to their elution times. Once separated, the major triterpene saponins were classified by their aglycone moieties and their structures tentatively identified based on their accurate mass spectra in positive and negative ESI mode. By the use of UHPLC coupled to a TOF, a high-resolution and accuracy mass analyzer, reliable molecular formulas of the detected compounds were predicted, and along with the generated MS spectra in full scan mode, allowed the tentative identification and classification of the most abundant triterpene saponins presented the samples analyzed. A rapid and comprehensive strategy to study the complex saponin profile is presented. Unlike other LC-MS/MS methods, the proposed method requires just one mass analyzer, and to our knowledge, this is the first systematic study on triterpene saponins in blackberry leaves. PMID: 30343243 [PubMed - as supplied by publisher]

Metabolomic alterations and oxidative stress are associated with environmental pollution in Procambarus clarkii.

Mon, 22/10/2018 - 14:56
Related Articles Metabolomic alterations and oxidative stress are associated with environmental pollution in Procambarus clarkii. Aquat Toxicol. 2018 Oct 13;205:76-88 Authors: Fernández-Cisnal R, García-Sevillano MA, García-Barrera T, Gómez-Ariza JL, Abril N Abstract Soils contaminated by toxic metallic elements from agricultural activities raise grave concern about their potential risk to human health through direct intake, bioaccumulation through the food chain, and their impacts on ecological systems. We have measured here the lipid and protein oxidation status and used metabolomic methodologies to identify and characterize the changes caused by metal pollution exposure in the digestive glands and gills of Procambarus clarkii, the red swamp crayfish. Specimens captured at two sites with intensive agriculture practices using diverse types of agrochemicals, located in the borders of Doñana Natural Park, were compared to ones caught in the core of the Park, a proven non-polluted place. As a highly metabolically active organ, the digestive gland accumulated more metallic elements than the gills and was consequently more affected at the metabolic level. Results also indicate that chronic pollution exposure generates oxidative stress and mitochondrial dysfunction that imposes a metabolic shift to enhanced aerobic glycolysis and lipid metabolism alteration. The integration of metabolomics with previous proteomic data gives a comprehensive vision of the metabolic disorders caused by chronic metal exposure to P. clarkii and identifies potential biomarkers useful for routine risk assessment of the aquatic ecosystems health. PMID: 30343212 [PubMed - as supplied by publisher]

Inhibition of ATP citrate lyase (ACLY) protects airway epithelia from PM2.5-induced epithelial-mesenchymal transition.

Mon, 22/10/2018 - 14:56
Related Articles Inhibition of ATP citrate lyase (ACLY) protects airway epithelia from PM2.5-induced epithelial-mesenchymal transition. Ecotoxicol Environ Saf. 2018 Oct 18;167:309-316 Authors: Fu Y, Lu R, Cui J, Sun H, Yang H, Meng Q, Wu S, Aschner M, Li X, Chen R Abstract Epidemiological studies have associated ambient fine particulate matter (PM2.5) exposure with lung cancer, in which epithelial-mesenchymal transition (EMT) is an initial process. Thus, it is important to identify the key molecule or pathway involved in the PM2.5 induced EMT. Human bronchial epithelial (HBE) cells were exposed to PM2.5 (100 or 500 μg/ml) for 30 passages and analyzed by metabolomics to identify the alteration of metabolites related to PM2.5 exposure. The expression levels of EMT markers were evaluated by qRT-PCR and Western blot assays in HBE cells and murine lung tissues. Reduced epithelial markers, increased mesenchymal markers expression levels and increased capacity of metastasis were observed in PM2.5-exposed HBE cells. Metabolomics analysis suggested upregulation of citrate acid with fold change (FC) of 2.89 or 4.18 in 100 or 500 μg/ml PM2.5 treated HBE cells. For both of the in vitro and in vivo study, the up-regulation of ATP citrate lyase (ACLY) was confirmed following PM2.5 exposure. Importantly, ACLY knockdown in HBE cells reversed EMT, migration and invasion capacities in HBE cells induced by PM2.5. Taken together, our data suggest that inhibition of ACLY demonstrates a protection against PM2.5-induced EMT, providing a concern on the molecular mechanisms of PM2.5-associated pulmonary disorders. PMID: 30343145 [PubMed - as supplied by publisher]

Microbiome and diabetes: Where are we now?

Sun, 21/10/2018 - 14:34
Related Articles Microbiome and diabetes: Where are we now? Diabetes Res Clin Pract. 2018 Oct 17;: Authors: Vallianou NG, Stratigou T, Tsagarakis S Abstract Alterations in the diversity or structure of gut microbiota known as dysbiosis, may affect metabolic activities, resulting in metabolic disorders, such as obesity and diabetes. The development of more sophisticated methods, such as metagenomics sequencing, PCR-denaturing gradient gel electrophoresis, microarrays and fluorescence in situ hybridization, has expanded our knowledge on gut microbiome. Dysbiosis has been related to increased plasma concentrations of gut microbiota-derived lipopolysaccharide (LPS), which triggers the production of a variety of cytokines and the recruitment of inflammatory cells. Metabolomics have demonstrated that butyrate and propionate suppress weight gain in mice with high fat diet-induced obesity, and acetate has been proven to reduce food intake in healthy mice. The role of prebiotics, probiotics, genetically modified bacteria and fecal microbiota transplantation, as potential therapeutic challenges for type 2 diabetes will be discussed in this review. PMID: 30342053 [PubMed - as supplied by publisher]

Advances in metabolic flux analysis toward genome-scale profiling of higher organisms.

Sun, 21/10/2018 - 14:34
Related Articles Advances in metabolic flux analysis toward genome-scale profiling of higher organisms. Biosci Rep. 2018 Oct 19;: Authors: Basler G, Fernie AR, Nikoloski Z Abstract Methodological and technological advances have recently paved the way for metabolic flux profiling in higher organisms, like plants. However, in comparison to omics technologies, flux profiling has yet to provide comprehensive differential flux maps at a genome-scale and in different cell types, tissues, and organs. Here we highlight the recent advances in technologies to gather metabolic labeling patterns and flux profiling approaches. We provide an opinion of how recent local flux profiling approaches can be used in conjunction with the constraint-based modelling framework to arrive at genome-scale flux maps. In addition, we point at approaches which use metabolomics data without introduction of label to predict either non-steady state fluxes in a time-series experiment or flux changes in different experimental scenarios. The combination of these developments allows an experimentally feasible approach for flux-based large-scale systems biology studies. PMID: 30341247 [PubMed - as supplied by publisher]

High-throughput chinmedomics strategy for discovering the quality-markers and potential targets for Yinchenhao decoction.

Sun, 21/10/2018 - 14:34
Related Articles High-throughput chinmedomics strategy for discovering the quality-markers and potential targets for Yinchenhao decoction. Phytomedicine. 2018 Apr 10;: Authors: Sun H, Zhang AH, Yang L, Li MX, Fang H, Xie J, Wang XJ Abstract BACKGROUND: Yinchenhao decoction (YCHD) has been widely applied in the clinic for various kinds of liver disease, especially for the therapy of dampness-heat jaundice syndrome (DHJS). Some studies have investigated the pharmacological activity and compositions of YCHD. However, its Q-markers and the action targets are still unrevealed. PURPOSE: This work aims to clarify the therapeutic effect of YCHD against DHJS and discover the quality-markers (Q-markers) of YCHD based on the high-throughput chinmedomics strategy and then predict the potential targets and action mechanism of YCHD against DHJS. METHODS: Ultra-high performance liquid chromatography/mass spectrometry (UPLC-MS) combined with pattern recognition method was utilized to analyze serum samples and urine samples. Multivariate data analysis and network pharmacology technology were used to identify the effective components and biomarkers associated with therapeutic effects. RESULTS: With the high sensitivity UPLC-MS technology, a total of 69 compounds from YCHD were identified and 41 of them were absorbed in blood. Besides, 34 urine biomarkers from DHJS were identified. Of note, we utilized chinmedomics technology on the correlation analysis of urine biomarkers and absorbed components to determine 9 core-compounds as the Q-markers responsible for the efficacy of YCHD. Finally, a total of 12 potential targets were discovered. CONCLUSION: This work provides a powerful method for clarifying the efficacy of TCM and discovering the effective ingredients as Q-markers. PMID: 30340940 [PubMed - as supplied by publisher]

Untargeted lipidomic features associated with colorectal cancer in a prospective cohort.

Sun, 21/10/2018 - 14:34
Related Articles Untargeted lipidomic features associated with colorectal cancer in a prospective cohort. BMC Cancer. 2018 Oct 19;18(1):996 Authors: Perttula K, Schiffman C, Edmands WMB, Petrick L, Grigoryan H, Cai X, Gunter MJ, Naccarati A, Polidoro S, Dudoit S, Vineis P, Rappaport SM Abstract BACKGROUND: Epidemiologists are beginning to employ metabolomics and lipidomics with archived blood from incident cases and controls to discover causes of cancer. Although several such studies have focused on colorectal cancer (CRC), they all followed targeted or semi-targeted designs that limited their ability to find discriminating molecules and pathways related to the causes of CRC. METHODS: Using an untargeted design, we measured lipophilic metabolites in prediagnostic serum from 66 CRC patients and 66 matched controls from the European Prospective Investigation into Cancer and Nutrition (Turin, Italy). Samples were analyzed by liquid chromatography-high-resolution mass spectrometry (LC-MS), resulting in 8690 features for statistical analysis. RESULTS: Rather than the usual multiple-hypothesis-testing approach, we based variable selection on an ensemble of regression methods, which found nine features to be associated with case-control status. We then regressed each selected feature on time-to-diagnosis to determine whether the feature was likely to be either a potentially causal biomarker or a reactive product of disease progression (reverse causality). CONCLUSIONS: Of the nine selected LC-MS features, four appear to be involved in CRC etiology and merit further investigation in prospective studies of CRC. Four other features appear to be related to progression of the disease (reverse causality), and may represent biomarkers of value for early detection of CRC. PMID: 30340609 [PubMed - in process]

¹H NMR Spectroscopy and MVA to Evaluate the Effects of Caulerpin-Based Diet on Diplodus sargus Lipid Profiles.

Sun, 21/10/2018 - 14:34
Related Articles ¹H NMR Spectroscopy and MVA to Evaluate the Effects of Caulerpin-Based Diet on Diplodus sargus Lipid Profiles. Mar Drugs. 2018 Oct 18;16(10): Authors: Del Coco L, Felline S, Girelli CR, Angilè F, Magliozzi L, Almada F, D'Aniello B, Mollo E, Terlizzi A, Fanizzi FP Abstract The biological invasion of the green algae Caulerpa cylindracea represents a serious scientific and public issue in the Mediterranean Sea, essentially due to strong modifications both to habitat structure and native benthic communities. Although alterations in health status and changes in flesh quality of some marine species (dietary exposed to C. cylindracea) have been observed, no studies on cause-effect relationships have been carried out. Here, for the first time, through a controlled feeding experiment followed by ¹H NMR Spectroscopy and multivariate analysis (PCA, OPLS-DA), we showed that caulerpin taken with diet is directly responsible of changes observed in metabolic profile of fish flesh, including alteration of lipid metabolism, in particular with a reduction of ω3 PUFA content. The potential of caulerpin to directly modulate lipid metabolism opens up new questions about causal mechanism triggered by algal metabolite also in view of a possible exploitation in the nutraceutical/medical field. PMID: 30340347 [PubMed - in process]

Probiotics in Autoimmune and Inflammatory Disorders.

Sun, 21/10/2018 - 14:34
Related Articles Probiotics in Autoimmune and Inflammatory Disorders. Nutrients. 2018 Oct 18;10(10): Authors: Liu Y, Alookaran JJ, Rhoads JM Abstract Probiotics have been used to ameliorate gastrointestinal symptoms since ancient times. Over the past 40 years, probiotics have been shown to impact the immune system, both in vivo and in vitro. This interaction is linked to gut microbes, their polysaccharide antigens, and key metabolites produced by these bacteria. At least four metabolic pathways have been implicated in mechanistic studies of probiotics, based on mechanistic studies in animal models. Microbial⁻immune system crosstalk has been linked to: short-chain fatty acid production and signaling, tryptophan metabolism and the activation of aryl hydrocarbon receptors, nucleoside signaling in the gut, and activation of the intestinal histamine-2 receptor. Several randomized controlled trials have now shown that microbial modification by probiotics may improve gastrointestinal symptoms and multiorgan inflammation in rheumatoid arthritis, ulcerative colitis, and multiple sclerosis. Future work will need to carefully assess safety issues, selection of optimal strains and combinations, and attempts to prolong the duration of colonization of beneficial microbes. PMID: 30340338 [PubMed - in process]

metabolomics; +37 new citations

Sat, 20/10/2018 - 14:07
37 new pubmed citations were retrieved for your search. Click on the search hyperlink below to display the complete search results: metabolomics These pubmed results were generated on 2018/10/20PubMed comprises more than millions of citations for biomedical literature from MEDLINE, life science journals, and online books. Citations may include links to full-text content from PubMed Central and publisher web sites.

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