HMDB 4.0: the human metabolome database for 2018

Nucleic Acids Research, Journal Year: 2017, Volume and Issue: 46(D1), P. D608 - D617

Published: Oct. 23, 2017

The Human Metabolome Database or HMDB (www.hmdb.ca) is a web-enabled metabolomic database containing comprehensive information about human metabolites along with their biological roles, physiological concentrations, disease associations, chemical reactions, metabolic pathways, and reference spectra. First described in 2007, the now considered standard resource for studies. Over past decade has continued to grow evolve response emerging needs metabolomics researchers continuing changes web standards. This year's update, 4.0, represents most significant upgrade its history. For instance, number of fully annotated increased by nearly threefold, experimental spectra grown almost fourfold illustrated pathways factor 60. Significant improvements have also been made HMDB's taxonomy, ontology, spectral viewing, spectral/text searching tools. A great deal brand new data added 4.0. includes large quantities predicted MS/MS GC-MS as well (physiologically feasible) metabolite structures facilitate novel identification. Additional on metabolite-SNP interactions influence drugs levels (pharmacometabolomics) added. Many other important content, interface, performance website these should greatly enhance ease use potential applications nutrition, biochemistry, clinical chemistry, genetics, medicine, science.

Language: Английский

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Emerging applications of metabolomics in drug discovery and precision medicine

Nature Reviews Drug Discovery, Journal Year: 2016, Volume and Issue: 15(7), P. 473 - 484

Published: March 11, 2016

Language: Английский

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Analysis of the Human Adult Urinary Metabolome Variations with Age, Body Mass Index, and Gender by Implementing a Comprehensive Workflow for Univariate and OPLS Statistical Analyses

Journal of Proteome Research, Journal Year: 2015, Volume and Issue: 14(8), P. 3322 - 3335

Published: June 19, 2015

Urine metabolomics is widely used for biomarker research in the fields of medicine and toxicology. As a consequence, characterization variations urine metabolome under basal conditions becomes critical order to avoid confounding effects cohort studies. Such physiological information however very scarce literature databases so far. Here we studied influence age, body mass index (BMI), gender on metabolite concentrations large 183 adults by using liquid chromatography coupled with high-resolution spectrometry (LC-HRMS). We implemented comprehensive statistical workflow univariate hypothesis testing modeling orthogonal partial least-squares (OPLS), which made available community within online Workflow4Metabolomics.org resource. found 108 metabolites displaying concentration either BMI, or gender, integrating results from p-values multivariate variable importance projection (VIP). Several clusters were further evidenced correlation analysis, they allowed stratification cohort. In conclusion, our study highlights impact age urinary metabolome, thus it indicates that these factors should be taken into account design

Language: Английский

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NMR Spectroscopy for Metabolomics Research

Metabolites, Journal Year: 2019, Volume and Issue: 9(7), P. 123 - 123

Published: June 27, 2019

Over the past two decades, nuclear magnetic resonance (NMR) has emerged as one of three principal analytical techniques used in metabolomics (the other being gas chromatography coupled to mass spectrometry (GC-MS) and liquid with single-stage (LC-MS)). The relative ease sample preparation, ability quantify metabolite levels, high level experimental reproducibility, inherently nondestructive nature NMR spectroscopy have made it preferred platform for long-term or large-scale clinical metabolomic studies. These advantages, however, are often outweighed by fact that most techniques, including both LC-MS GC-MS, more sensitive than NMR, lower limits detection typically 10 100 times better. This review is intended introduce readers field NMR-based highlight advantages disadvantages It will also explore some unique strengths metabolomics, particularly regard isotope selection/detection, mixture deconvolution via 2D spectroscopy, automation, noninvasively analyze native tissue specimens. Finally, this a number emerging technologies strengthen its utility overcome inherent limitations applications.

Language: Английский

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Guidelines for the use of flow cytometry and cell sorting in immunological studies (second edition)

European Journal of Immunology, Journal Year: 2019, Volume and Issue: 49(10), P. 1457 - 1973

Published: Oct. 1, 2019

These guidelines are a consensus work of considerable number members the immunology and flow cytometry community. They provide theory key practical aspects enabling immunologists to avoid common errors that often undermine immunological data. Notably, there comprehensive sections all major immune cell types with helpful Tables detailing phenotypes in murine human cells. The latest techniques applications also described, featuring examples data can be generated and, importantly, how analysed. Furthermore, tips, tricks pitfalls avoid, written peer-reviewed by leading experts field, making this an essential research companion.

Language: Английский

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Metabolomics for Investigating Physiological and Pathophysiological Processes

Physiological Reviews, Journal Year: 2019, Volume and Issue: 99(4), P. 1819 - 1875

Published: Aug. 22, 2019

Metabolomics uses advanced analytical chemistry techniques to enable the high-throughput characterization of metabolites from cells, organs, tissues, or biofluids. The rapid growth in metabolomics is leading a renewed interest metabolism and role that small molecule play many biological processes. As result, traditional views as being simply “bricks mortar” cells just fuel for cellular energetics are upended. Indeed, appear have much more varied far important roles signaling molecules, immune modulators, endogenous toxins, environmental sensors. This review explores how yielding new insights into number physiological In particular, major focus on illustrating discoveries made through improving our understanding both normal physiology pathophysiology diseases. These influence organ function, nutrient sensing, gut physiology. Collectively, this work unified system-wide perspective biology wherein metabolites, proteins, genes understood interact synergistically modify actions functions organelles, organisms.

Language: Английский

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Analytical Methods in Untargeted Metabolomics: State of the Art in 2015

Frontiers in Bioengineering and Biotechnology, Journal Year: 2015, Volume and Issue: 3

Published: March 5, 2015

Metabolomics comprises the methods and techniques that are used to measure small molecule composition of biofluids tissues, is actually one most rapidly evolving research fields. The determination metabolomic profile –the metabolome- has multiple applications in many biological sciences, including developing new diagnostic tools medicine. Recent technological advances nuclear magnetic resonance (NMR) mass spectrometry (MS) significantly improving our capacity obtain more data from each sample. Consequently, there a need for fast accurate statistical bioinformatic can deal with complexity volume generated studies. In this review we provide an update commonly analytical metabolomics, starting raw processing ending pathway analysis biomarker identification. Finally, integration profiles molecular other high throughput biotechnologies also reviewed.

Language: Английский

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The Strengths and Weaknesses of NMR Spectroscopy and Mass Spectrometry with Particular Focus on Metabolomics Research

Methods in molecular biology, Journal Year: 2015, Volume and Issue: unknown, P. 161 - 193

Published: Jan. 1, 2015

Language: Английский

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Treating inflammation and infection in the 21st century: new hints from decoding resolution mediators and mechanisms

The FASEB Journal, Journal Year: 2017, Volume and Issue: 31(4), P. 1273 - 1288

Published: Jan. 13, 2017

Practitioners of ancient societies from the time Hippocrates and earlier recognized treated signs inflammation, heat, redness, swelling, pain with agents that block or inhibit proinflammatory chemical mediators. More selective drugs are available today, but this therapeutic concept has not changed. Because acute inflammatory response is host protective to contain foreign invaders, much today's pharmacopeia can cause serious unwanted side effects, such as immune suppression. Uncontrolled inflammation now considered path-ophysiologic associated many widely occurring diseases cardiovascular disease, neurodegen-erative diseases, diabetes, obesity, asthma, well classic (e.g., arthritis periodontal diseases). The response, when self-limited, produces a superfamily media-tors stimulate resolution response. Specialized proresolving mediators (SPMs), identified in recent years, endogenous include n-3–derived families resolvins, protectins, maresins, arachidonic acid–derived (n-6) lipoxins, which promote clearance microbes, reduction pain, promotion tissue regeneration via novel mechanisms. Aspirin statins have positive impact on these pathways, producing epimeric forms specific SPMs, whereas other disrupt timely resolution. In article, evidence human preclinical animal studies reviewed, indicating SPMs physiologic pharmacologic agonists infection. findings suggest it challenge current treatment practices—namely, using inhibitors antagonists alone—and develop immunoresolvents test pharmacology their role catabasis for potential. —Serhan, C. N. Treating infection 21st century: new hints decoding FASEB J. 31, 1273–1288 (2017) www.fasebj.org

Language: Английский

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FODMAPs alter symptoms and the metabolome of patients with IBS: a randomised controlled trial

Gut, Journal Year: 2016, Volume and Issue: 66(7), P. 1241 - 1251

Published: March 14, 2016

Objective To gain mechanistic insights, we compared effects of low fermentable oligosaccharides, disaccharides and monosaccharides polyols (FODMAP) high FODMAP diets on symptoms, the metabolome microbiome patients with IBS. Design We performed a controlled, single blind study IBS (Rome III criteria) randomised to (n=20) or diet for 3 weeks. Symptoms were assessed using symptom severity scoring (IBS-SSS). The was evaluated lactulose breath test (LBT) metabolic profiling in urine mass spectrometry. Stool microbiota composition analysed by 16S rRNA gene profiling. Results Thirty-seven (19 FODMAP; 18 FODMAP) completed 3-week diet. IBS-SSS reduced group (p<0.001) but not group. LBTs showed minor decrease H 2 production Metabolic groups differed significantly after (p<0.01), three metabolites (histamine, p-hydroxybenzoic acid, azelaic acid) being primarily responsible discrimination between two groups. Histamine, measure immune activation, eightfold (p<0.05). Low increased Actinobacteria richness diversity, decreased relative abundance bacteria involved gas consumption. Conclusions symptoms are linked content associated alterations metabolome. In subsets patients, FODMAPs modulate histamine levels microbiota, both which could alter symptoms. Trial registration number NCT01829932.

Language: Английский

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