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

PubMed
NCBI: db=pubmed; Term=metabolomics
Updated: 15 min 14 sec ago

Power-efficient self-cleaning hydrophilic condenser surface for portable exhaled breath condensate (EBC) metabolomic sampling.

Sat, 10/08/2019 - 13:26
Related Articles Power-efficient self-cleaning hydrophilic condenser surface for portable exhaled breath condensate (EBC) metabolomic sampling. J Breath Res. 2018 06 08;12(3):036020 Authors: Zamuruyev KO, Schmidt AJ, Borras E, McCartney MM, Schivo M, Kenyon NJ, Delplanque JP, Davis CE Abstract In this work, we present a hydrophilic self-cleaning condenser surface for the collection of biological and environmental aerosol samples. The condenser is installed in a battery-operated hand-held breath sampling device. The device performance is characterized by the collection and analysis of exhaled breath samples from a group of volunteers. The exhaled breath condensate is collected on a subcooled condenser surface, transferred into a storage vial, and its chemical content is analyzed using mass spectrometric methods. The engineered surface supports upon it a continuous condensation cycle, and this allows the collection of liquid samples exceeding the saturation mass/area limit of a plain hydrophilic surface. The condenser surface employs two constituent parameters: a low surface energy barrier to enhance nucleation and condensation efficiency, and a network of surface microstructures to create a self-cleaning mechanism for fluid aggregation into a reservoir. Removal of the liquid condensate from the condenser surface prevents the formation of a thick liquid layer, and thus maintains a continuous condensation cycle with a minimum decrease in heat transfer efficiency as condensation occurs on the surface. The self-cleaning condenser surfaces may have a number of applications in the collection of biological, chemical, or environmental aerosol samples. Sample phase conversion to liquid can facilitate sample manipulation and chemical analysis of matrices with low concentrations. Here, we demonstrate the use of a self-cleaning microcondenser for the collection of exhaled breath condensate with a hand-held portable device. All breath collections with the two devices were performed with the same group of volunteers under UC Davis IRB protocol 63701-3. PMID: 29771240 [PubMed - indexed for MEDLINE]

metabolomics; +16 new citations

Fri, 09/08/2019 - 13:15
16 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 2019/08/09PubMed 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; +26 new citations

Thu, 08/08/2019 - 13:05
26 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 2019/08/08PubMed 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; +25 new citations

Wed, 07/08/2019 - 15:53
25 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 2019/08/07PubMed 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; +25 new citations

Wed, 07/08/2019 - 12:53
25 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 2019/08/07PubMed 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; +18 new citations

Tue, 06/08/2019 - 21:45
18 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 2019/08/06PubMed 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; +18 new citations

Tue, 06/08/2019 - 12:41
18 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 2019/08/06PubMed 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.

Mass spectrometry-based metabolomics approach to reveal differential compounds in pufferfish soups: Flavor, nutrition, and safety.

Mon, 05/08/2019 - 12:17
Mass spectrometry-based metabolomics approach to reveal differential compounds in pufferfish soups: Flavor, nutrition, and safety. Food Chem. 2019 Jul 26;301:125261 Authors: Bi H, Cai D, Zhang R, Zhu Y, Zhang D, Qiao L, Liu Y Abstract Some Eastern Asian countries deem pufferfish - especially its muscle - a culinary delight. Herein, molecular mass fingerprinting of soups prepared by Takifugu flavidus, Takifugu obscurus and Takifugu rubripes was established via matrix-assisted laser desorption/ionization - mass spectrometry (MALDI MS). Soup samples were directly analyzed by MALDI MS to collect mass spectra within 0-700 Da in a quick way, followed by principal component analysis to distinguish the different soups and to find out the distinctive compounds among the soups. High performance liquid chromatography - tandem MS (HPLC-MS/MS) was applied to identify the compounds. Nineteen compounds were identified from the HPLC-MS/MS data by using METLIN database. Through literature mining, we found that these compounds are closely related to the flavor, nutrition, and safety of pufferfish soups. This method can also be used as a facile way to distinguish between different pufferfish fillets when morphological characters have been damaged or destroyed. PMID: 31377618 [PubMed - as supplied by publisher]

The response of the algae Fucus virsoides (Fucales, Ochrophyta) to Roundup® solution exposure: A metabolomics approach.

Mon, 05/08/2019 - 12:17
The response of the algae Fucus virsoides (Fucales, Ochrophyta) to Roundup® solution exposure: A metabolomics approach. Environ Pollut. 2019 Jul 27;254(Pt A):112977 Authors: Felline S, Del Coco L, Kaleb S, Guarnieri G, Fraschetti S, Terlizzi A, Fanizzi FP, Falace A Abstract Glyphosate, as a broad-spectrum herbicide, is frequently detected in water and several studies have investigated its effects on several freshwater aquatic organisms. Yet, only few investigations have been performed on marine macroalgae. Here, we studied both the metabolomics responses and the effect on primary production in the endemic brown algae Fucus virsoides exposed to different concentration (0, 0.5, 1.5 and 2.5 mg L-1) of a commercial glyphosate-based herbicide, namely Roundup®. Our results show that Roundup® significantly reduced quantum yield of photosynthesis (Fv/Fm) and caused alteration in the metabolomic profiles of exposed thalli compared to controls. Together with the decrease in the aromatic amino acids (phenylalanine and tyrosine), an increase in shikimate content was detected. The branched-amino acids differently varied according to levels of herbicide exposure, as well as observed for the content of choline, formate, glucose, malonate and fumarate. Our results suggest that marine primary producers could be largely affected by the agricultural land use, this asking for further studies addressing the ecosystem-level effects of glyphosate-based herbicides in coastal waters. PMID: 31377326 [PubMed - as supplied by publisher]

Beneficial effects of Oridonin on myocardial ischemia/reperfusion injury: Insight gained by metabolomic approaches.

Mon, 05/08/2019 - 12:17
Beneficial effects of Oridonin on myocardial ischemia/reperfusion injury: Insight gained by metabolomic approaches. Eur J Pharmacol. 2019 Aug 01;:172587 Authors: Zhang J, Zhou Y, Sun Y, Yan H, Han W, Wang X, Wang K, Wei B, Xu X Abstract Oridonin is a diterpenoid isolated from Rabdosia rubescens (Hemsl.) Hara, a well-known herbal tea in China with many health benefits. To provide a better understanding of the potential cardioprotective effect of Oridonin, we investigated the metabolic alterations in heart tissue and serum of rat subjected to myocardial ischemia/reperfusion (MI/R) injury with or without pretreatment of Oridonin by UPLC-MS/MS metabolomics approach. Rats were randomly divided into groups as follows: Control, Sham, MI/R and pretreated with Oridonin (10 mg/kg)+MI/R. After 24 h of reperfusion, heart tissue and serum were collected for biochemical and metabolomic analysis. Pretreatment with Oridonin significantly decreased infarct size and reversed the abnormal elevated myocardial zymogram in serum. Moreover, Oridonin regulated several metabolic pathways, including glycolysis, branched chain amino acid, kynurenine, arginine, glutamine and bile acid metabolism. Our results suggest that Oridonin indeed displays outstanding cardioprotective effect mainly by regulating energy and amino acid metabolism. PMID: 31377155 [PubMed - as supplied by publisher]

NMR metabolomics: A look ahead.

Mon, 05/08/2019 - 12:17
NMR metabolomics: A look ahead. J Magn Reson. 2019 Jul 11;: Authors: Wishart DS Abstract NMR has been used to perform metabolic studies, metabolic profiling and metabolomics in biofluids and tissues for more than 40 years. This close connection between metabolic measurements and NMR has flourished because of NMR's many unique strengths for characterizing the chemical composition of complex mixtures. However, a number of other technologies, including mass spectrometry, have appeared in the past few years that are encroaching on NMR's dominance in metabolomics and metabolic studies. In this brief review, some of the current strengths and existing limitations of NMR-based metabolomics are highlighted. Additionally, a number of recent advances in NMR hardware, methodology and software are also described and these advancements are used to speculate about where NMR-based metabolomics is going, what needs to be done to make it more popular and how it will evolve in the next 5-10 years. PMID: 31377153 [PubMed - as supplied by publisher]

Metabolomic changes and polyunsaturated fatty acid biosynthesis during gonadal growth and development in the sea urchin Strongylocentrotus intermedius.

Sun, 04/08/2019 - 12:07
Metabolomic changes and polyunsaturated fatty acid biosynthesis during gonadal growth and development in the sea urchin Strongylocentrotus intermedius. Comp Biochem Physiol Part D Genomics Proteomics. 2019 Jul 26;32:100611 Authors: Wang H, Ding J, Ding S, Chang Y Abstract Strongylocentrotus intermedius is an important commercial species of sea urchin distributed in the coastal waters of China. However, the metabolomic changes that accompany its gonadal growth and development stages remain unclear. In this study, we have histologically observed gonad growth stages, analyzed the fatty acid composition, and employed an untargeted metabolomic approach to investigate the metabolites associated with the gonadal growth and development of S. intermedius, as well as the biosynthesis and metabolism of polyunsaturated fatty acids (PUFAs) at different stages and in different sexes. The gonad mass of sea urchin increased from 0.70 ± 0.18 g in January (at the recovering stage) to 8.78 ± 2.89 g in July (the reproductive stage), with the GSI increasing from 4.02 ± 0.88% to 16.86 ± 2.79%. We have analyzed 34 types of fatty acids, such as arachidonic acid, eicosapentaenoic acid, etc., of which PUFAs were the dominant fatty acid class in this species, accounting for >48.55% of the total. In the metabolomic analysis, linolelaidic acid, sciadonic acid, cis-8,11,14,17-eicosatetraenoic acid, adrenic acid, docosapentaenoic acid, and tetracosapentaenoic acid were detected in the differentially expressed metabolites of the unsaturated fatty acids biosynthesis pathway. We found that the most significant functional pathways during gonadal growth and development were "arachidonic acid metabolism", "alpha-linolenic acid metabolism" and "linoleic acid metabolism", which are all related to fatty acid metabolism. These results will provide valuable information on the possible presence of both exogenous and endogenous fatty acids in sea urchin gonads and the metabolomic changes in S. intermedius during gonadal growth periods, and will further our understanding of the intermediary metabolism and the molecular bases of growth traits in this species. PMID: 31376663 [PubMed - as supplied by publisher]

Identification of Altered Metabolic Pathways during Disease Progression in EAE Mice Via Metabolomics and Lipidomics.

Sun, 04/08/2019 - 12:07
Identification of Altered Metabolic Pathways during Disease Progression in EAE Mice Via Metabolomics and Lipidomics. Neuroscience. 2019 Jul 31;: Authors: Lee G, Hasan M, Kwon OS, Jung BH Abstract Multiple sclerosis (MS) is a demyelination disease that causes gradual damage to neurons. Despite the necessity of appropriate treatments at each disease stage to prevent the worsening of the damage, it is still difficult to cure MS. In this study, metabolomics and lipidomics studies were performed with time-course plasma samples (early, peak, chronic phase for MS) to elucidate the mechanism during MS progression after induction of experimental autoimmune encephalomyelitis (EAE), which is the animal model for multiple sclerosis (MS). Plasma samples were analyzed using ultra-high performance liquid chromatography-orbitrap-mass spectrometry (UHPLC-Orbitrap-MS) and metabolic changes were observed using multivariate analysis. We also measured the activity of NADPH and MMP-9 to evaluate the degree of the inflammation during the disease progression. As a results, 49 metabolites, which had significant differences either at each time point or with time-course changes between control (CTL) and EAE groups, were identified. Among them, glycerophospholipids and fatty acyls were downregulated during disease progression compared with the CTL group. However, glycerolipids, taurine-conjugated bile acids (BAs), and sphingolipids exhibited the reverse pattern. These metabolic changes were accompanied by increases in oxidative stress and immune response upon observing the changes in the activities of NADPH oxidase and MMP-9. In particular, 26 metabolites showed significant differences at specific stages. The metabolite level of the plasma was significantly altered in response to the EAE pathogenesis, and these changes were related to inflammation status at each disease stage. This study can provide crucial information for reducing damage by differentiating treatment strategies according to disease progression. PMID: 31376423 [PubMed - as supplied by publisher]

Comparison of Five Extraction Methods for Intracellular Metabolites of Salmonella typhimurium.

Sun, 04/08/2019 - 12:07
Related Articles Comparison of Five Extraction Methods for Intracellular Metabolites of Salmonella typhimurium. Curr Microbiol. 2019 Aug 02;: Authors: Tian S, Wang C, Yang L, Zhang Y, Tang T Abstract Salmonella enterica serovar typhimurium (S. typhimurium) causes food poisoning in human and animals. Its infection rate is the highest among all salmonella serotypes. Metabolomics is a potential way to study the pathogenesis of S. typhimurium via analysis of various small molecular substances. Due to the lack of a uniform protocol for the extraction of metabolites, we evaluated five commonly used extraction methods including cold methanol (CM), hot ethanol (HE), chloroform-methanol cocktail (CMC), perchloric acid (PCA), and alkali (AL) for their efficacy in extracting the intracellular metabolites of S. typhimurium. Samples were quenched in 60% methanol at - 40 °C, and then the five methods were used to extract the metabolites. After derivatization, all samples were analyzed on a gas chromatography-triple quadrupole mass spectrometry (GC-MS/MS). Our results suggest that CM and HE extraction methods provide the best compromise allowing identification of 98 and 95 metabolites in a single analysis. For targeted metabolome analysis, the optimal extraction method for alcohols and organic acids is HE. CMC preferentially extracted lipid metabolites. PCA is suitable for extraction of small molecular carbohydrates. The optimal extraction method for macromolecular carbohydrates is the CM method. PMID: 31375861 [PubMed - as supplied by publisher]

Climate and development modulate the metabolome and anti-oxidative system of date palm leaves.

Sun, 04/08/2019 - 12:07
Related Articles Climate and development modulate the metabolome and anti-oxidative system of date palm leaves. J Exp Bot. 2019 Aug 03;: Authors: Du B, Kruse J, Winkler JB, Alfarray S, Schnitzler JP, Ache P, Hedrich R, Rennenberg H Abstract Date palms are remarkably tolerant to environmental stresses, but the mechanisms involved remain poorly characterised. Leaf metabolome profiling was therefore performed on mature (ML) and young (YL) leaves of two-year-old date palm seedlings that had been grown in climate chambers that simulate summer and winter conditions in eastern Saudi Arabia. Cultivation under high temperature (summer climate) resulted in higher YL H2O2 leaf levels despite increases in dehydroascorbate reductase (DHAR) activities. The levels of raffinose and galactinol abundances, tricarboxylic acid cycle intermediates, and total amino acid were higher under these conditions, particularly in YL. The accumulation of unsaturated fatty acids, 9,12-octadecadienoic acid and 9,12,15-octadecatrienoic acid was lower in ML. In contrast, the amounts of saturated tetradecanoic acid and heptadecanoic acid were increased in YL under summer climate conditions. The accumulation of phenolic compounds was favored under summer conditions, while flavonoids accumulated under lower temperature (winter climate) conditions. YL displayed stronger hydration, lower H2O2 levels and more negative δ13C values indicating effective reactive oxygen species scavenging. These findings, which demonstrate the substantial metabolic adjustments that facilitate tolerance to the high temperatures in YL and ML, suggest that YL may be more responsive to climate change. PMID: 31375818 [PubMed - as supplied by publisher]

Amino acids and wound healing in people with limb-threatening diabetic foot ulcers.

Sun, 04/08/2019 - 12:07
Related Articles Amino acids and wound healing in people with limb-threatening diabetic foot ulcers. J Diabetes Complications. 2019 Jul 06;:107403 Authors: Hung SY, Tsai JS, Yeh JT, Chen KH, Lin CN, Yang HM, Lin CW, Chen HY, Huang CH, Huang YY Abstract BACKGROUND: Amino acids are associated with wound healing in traumatic wounds and burns, although their effects on healing in patients with diabetic foot ulcers (DFUs) are limited. This study aimed to evaluate and identify specific amino acids associated with healing outcomes of patients with DFUs. METHODS: Sixty-two out of 85 patients who completed the in-hospital treatment for limb-threatening DFUs were enrolled. All ulcers had epithelialization without clinical evidence of infection at discharge. The patients and their families were instructed on foot-care techniques and committed to regular follow-up for 1 year. Baseline characteristics, PEDIS wound classification, laboratory data and serum amino acid levels were used to analyze their predictive power. RESULTS: Fifty-seven patients completed the study in which 38 had healed and 19 had unhealed ulcers. The unhealed group had higher incidence of coronary artery disease and larger wound size. Most patients received endovascular therapy (81.6% healed group; 78.9% unhealed group) before enrollment. Following adjustments for clinical factors, the serum levels of arginine (326.4 μmol/L vs. 245.0 μmol/L, P = 0.045), isoleucine (166.7 μmol/L vs. 130.1 μmol/L, P = 0.019), leucine (325.8 μmol/L vs. 248.9 μmol/L, P = 0.039), and threonine (186.7 μmol/L vs. 152.0 μmol/L, P = 0.019) were significantly higher in the healed group. CONCLUSIONS: The amino acids associated with wound healing in DFUs differ from those reported for traditional traumatic wounds. These findings affirm the necessity for future large-scaled studies for the application of these amino acids in DFU healing, either as prognostic predictors or supplemented regimens. PMID: 31375421 [PubMed - as supplied by publisher]

Comparative Metabolomic Analysis of Rapeseeds from Three Countries.

Sun, 04/08/2019 - 12:07
Related Articles Comparative Metabolomic Analysis of Rapeseeds from Three Countries. Metabolites. 2019 Aug 01;9(8): Authors: Yang R, Deng L, Zhang L, Yue X, Mao J, Ma F, Wang X, Zhang Q, Zhang W, Li P Abstract Rapeseed is an important oilseed with proper fatty acid composition and abundant bioactive components. Canada and China are the two major rapeseed-producing countries all over the world. Meanwhile, Canada and Mongolia are major importers of rapeseed due to the great demand for rapeseed in China. To investigate the metabolites in rapeseeds from three countries, ultra-performance liquid chromatography-quadrupole time-of-flight mass spectrometry (UPLC-Q-TOF/MS)-based metabolomics was employed to analyze rapeseeds from China, Canada, and Mongolia. As results, 67, 53, and 68 metabolites showed significant differences between Chinese and Canadian, Chinese and Mongolian, and Canadian and Mongolian rapeseeds, respectively. Differential metabolites were mainly distributed in the metabolic pathways including phenylpropanoid biosynthesis, flavone and flavonol biosynthesis, and ubiquinone and other terpenoid-quinone biosynthesis. Among the differential metabolites, contents of sinapate and sinapine were higher in Chinese rapeseeds, while the contents of brassicasterol, stigmasterol, and campestanol were higher in Canadian rapeseeds. These findings might provide insight into the metabolic characteristics of rapeseeds from three countries to guide processing and consumption of the products of rapeseed. PMID: 31374906 [PubMed]

Omics Meeting Onics: Towards the Next Generation of Spectroscopic-Based Technologies in Personalized Medicine.

Sun, 04/08/2019 - 12:07
Related Articles Omics Meeting Onics: Towards the Next Generation of Spectroscopic-Based Technologies in Personalized Medicine. J Pers Med. 2019 Aug 01;9(3): Authors: Peng WK, Paesani D Abstract This article aims to discuss the recent development of integrated point-of-care spectroscopic-based technologies that are paving the way for the next generation of diagnostic monitoring technologies in personalized medicine. Focusing on the nuclear magnetic resonance (NMR) technologies as the leading example, we discuss the emergence of -onics technologies (e.g., photonics and electronics) and how their coexistence with -omics technologies (e.g., genomics, proteomics, and metabolomics) can potentially change the future technological landscape of personalized medicine. The idea of an open-source (e.g., hardware and software) movement is discussed, and we argue that technology democratization will not only promote the dissemination of knowledge and inspire new applications, but it will also increase the speed of field implementation. PMID: 31374867 [PubMed]

Tear Metabolomics in Dry Eye Disease: A Review.

Sun, 04/08/2019 - 12:07
Related Articles Tear Metabolomics in Dry Eye Disease: A Review. Int J Mol Sci. 2019 Aug 01;20(15): Authors: Yazdani M, Elgstøen KBP, Rootwelt H, Shahdadfar A, Utheim ØA, Utheim TP Abstract Dry eye disease (DED) is a multifactorial syndrome that can be caused by alteration in the quality or quantity of the precorneal tear film. It is considered one of the most common ocular conditions leading patients to seek eye care. The current method for diagnostic evaluations and follow-up examinations of DED is a combination of clinical signs and symptoms determined by clinical tests and questionnaires, respectively. The application of powerful omics technologies has opened new avenues toward analysis of subjects in health and disease. Metabolomics is a new emerging and complementary research discipline to all modern omics in the comprehensive analysis of biological systems. The identification of distinct metabolites and integrated metabolic profiles in patients can potentially inform clinicians at an early stage or during monitoring of disease progression, enhancing diagnosis, prognosis, and the choice of therapy. In ophthalmology, metabolomics has gained considerable attention over the past decade but very limited such studies have been reported on DED. This paper aims to review the application of tear metabolomics in DED. PMID: 31374809 [PubMed - in process]

metabolomics; +17 new citations

Sat, 03/08/2019 - 14:54
17 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 2019/08/03PubMed 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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