An Overview of Metabolic Phenotyping and Its Role in Systems Biology

Holmes, Elaine; Wilson, Ian D.; Lindon, John C.

doi:10.1016/b978-0-12-812293-8.00001-3

Cited by 5 publications

(2 citation statements)

References 251 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The combination of the genome, transcriptome, proteome, and metabolome determines the phenotype of any species [1]. Metabolomics is one of the youngest fields of '-omics' sciences, aimed at identifying and quantifying as many metabolites as possible in biological tissues and fluids.…”

Section: Introductionmentioning

confidence: 99%

Animal Metabolite Database: Metabolite Concentrations in Animal Tissues and Convenient Comparison of Quantitative Metabolomic Data

Yanshole,

Melnikov,

Yanshole

et al. 2023

Metabolites

View full text Add to dashboard Cite

The Animal Metabolite Database (AMDB, https://amdb.online) is a freely accessible database with built-in statistical analysis tools, allowing one to browse and compare quantitative metabolomics data and raw NMR and MS data, as well as sample metadata, with a focus on the metabolite concentrations rather than on the raw data itself. AMDB also functions as a platform for the metabolomics community, providing convenient deposition and exchange of quantitative metabolomic data. To date, the majority of the data in AMDB relate to the metabolite content of the eye lens and blood of vertebrates, primarily wild species from Siberia, Russia and laboratory rodents. However, data on other tissues (muscle, heart, liver, brain, and more) are also present, and the list of species and tissues is constantly growing. Typically, every sample in AMDB contains concentrations of 60–90 of the most abundant metabolites, provided in nanomoles per gram of wet tissue weight (nmol/g). We believe that AMDB will become a widely used tool in the community, as typical metabolite baseline concentrations in tissues of animal models will aid in a wide variety of fundamental and applied scientific fields, including, but not limited to, animal modeling of human diseases, assessment of medical formulations, and evolutionary and environmental studies.

show abstract

Section: Introductionmentioning

confidence: 99%

Animal Metabolite Database: Metabolite Concentrations in Animal Tissues and Convenient Comparison of Quantitative Metabolomic Data

Yanshole,

Melnikov,

Yanshole

et al. 2023

Metabolites

View full text Add to dashboard Cite

show abstract

“…Metabolomics describes the metabolic composition of samples present at diverse concentrations, while the term metabolome is the multivariate sum of these components (Fiehn, 2002;Zhang et al, 2011;Nicholson et al, 2012;Xia et al, 2015). These analyses are considered quantitative measurements of the dynamic multiparametric metabolic response of living systems to environmental stimuli or genetic modification (Fiehn et al, 2000;Roessner et al, 2001;Holmes et al, 2019). Metabolic phenotyping involves the comprehensive analysis of biological fluids or tissue samples (Roullier-Gall et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

Trunk Girdling Increased Stomatal Conductance in Cabernet Sauvignon Grapevines, Reduced Glutamine, and Increased Malvidin-3-Glucoside and Quercetin-3-Glucoside Concentrations in Skins and Pulp at Harvest

et al. 2020

View full text Add to dashboard Cite

Girdling is a traditional horticultural practice applied at fruit set or other phenological stages, and is used mostly as a vine management. In grapevines, it is used primarily for table grapes to improve berry weight, sugar content, color, and to promote early harvest. The objective of this study was to evaluate the effect of trunk girdling applied at veraison, in 'Cabernet Sauvignon' wine grapes (Vitis vinifera L.), on agronomical and physiological parameters during vine development from the onset of ripening (veraison) to harvest, and additionally to quantify the effect of girdling on primary and secondary metabolism. Girdling was applied 146 days after pruning (dap) at veraison, when berry sampling for metabolomics and agronomical evaluations commenced, with a further three sampling dates until harvest, at 156 dap (30% maturation, 10 days after girdling-dag), 181 dap (70% maturation, 35 dag), and 223 dap (commercial harvest, 77 dag). Skin/pulp and seed tissues were extracted separately and metabolomics was performed using one-dimensional proton nuclear magnetic resonance (1D 1 H NMR) spectroscopy and high performance liquid chromatography (HPLC-DAD). At harvest, girdling significantly increased stomatal conductance (g s ) in vines, decreased glutamine concentrations, and increased anthocyanin and flavonol concentrations in the skin/pulp tissues of grape berries. Berry weight was reduced by 27% from 181 dap to harvest, and was significantly higher in grapes from girdled vines at 181 dap. Sugars, organic acids, and other amino acids in skin/pulp or seeds were not significantly different, possibly due to extra-fascicular phloem vessels transporting metabolites from leaves

show abstract