metabolomics

Viewing posts tagged metabolomics

27 Oct 2021

New study asks “Do oral diseases correlate with other health outcomes?”

By nickwiecien

The human mouth harbors a wide variety of microbes – over 700 kinds. These bacteria are in saliva, on the tongue and cheeks, on the tooth surface and under the gums. The development of plaque is particularly important in diseases like tooth decay and gum disease. The oral microbiota that contribute to these disease are also correlated with other diseases, including diabetes, arthritis, and heart disease, suggesting they have a broad impact on human health. This study analyzed the microbiome, proteome, lipidome, and metabolome of dental plaque samples from individuals with periodontal disease and pre- and type 2 diabetes.

Read the article: Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease.

Read the article: Proteomics, lipidomics, metabolomics and 16S rDNA sequencing of dental plaque from patients with diabetes and periodontal disease

25 Aug 2021

The science behind how soy sauce tastes

By nickwiecien

Soy sauce is a naturally fermented global condiment. It is complex in its chemical profile of salts and organic compounds, but is susceptible to deterioration after bottling. This study by Reddy et al. examined soy sauces over an eight-month period using sensory testing, such as taste and smell, and identifying metabolomic biomarkers using mass spectrometry. They found that changes in soy sauce resulting from storage have decreases in fruity/grape and nutty/sesame taste and aroma, increases in methional/potato aroma and astringent attributes. These taste and smell differences were confirmed with mass spectrometry, which identified changes in the concentrations of several key biomarkers.

Read the article: Metabolomic Biomarkers Differentiate Soy Sauce Freshness under Conditions of Accelerated Storage

17 Mar 2021

Achieving a simplified, multi-omics workflow

By nickwiecien

An article by Yuchen He et. al. titled “Multi-omic Single-Shot Technology for Integrated Proteome and Lipidome Analysis” was recently published as one of the cover stories in Analytical Chemistry.

This article describes a technology to achieve broad and deep coverage of multiple molecular classes simultaneously through Multi-omics (proteome, lipidome, and metabolome) single-shot technology (MOST), requiring only one column, one LC-MS instrument, and a simplified workflow.

02 Sep 2020

Li lab identifies metabolite and protein biomarkers to identify prostatic inflammation with lower urinary tract symptoms

By nickwiecien

Lower urinary tract symptoms (LUTS) are common among aging men. Since inflammation is one of its indicators, it is plausible that urinary metabolite and protein biomarkers could be used to identified and diagnose inflammation-induced LUTS. In this study, the Li lab used Mass spectrometry (MS)-based multi-omics analysis to characterize the urine metabolome and proteome in a mouse model. By comparing their findings with urinary biomarkers associated with LUTS in older men, they identified creatine, haptoglobin, immunoglobulin kappa constant and polymeric Ig receptor as conserved biomarkers for prostatic inflammation associated with LUTS.

The full article, Urinary metabolomic and proteomic analyses in a mouse model of prostatic inflammation, can be viewed here.

17 Jun 2020

Collaboration with Puglielli lab reveals AT-1 acts as metabolic regulator for acetyl-CoA

By nickwiecien

In a paper titled Acetyl-CoA Flux Regulates the Proteome and Acetyl-Proteome to Maintain Intracellular Metabolic Crosstalk, Inca Dieterich et al. of Prof Luigi Puglielli’s lab investigated two models of AT-1 dysregulation and altered acetyl-CoA flux: AT-1S113R/+ mice, a model of AT-1 haploin sufficiency, and AT-1 sTg mice, a model of AT-1 overexpression. The animals display distinct metabolic adaptation across intracellular compartments, including reprogramming of lipid metabolism and mitochondria bioenergetics. Our results suggest that AT-1 acts as an important metabolic regulator that maintains acetyl-CoA homeostasis by promoting functional crosstalk between different intracellular organelles.

03 Jun 2020

Collaboration Yields Insight on Role of Metabolism in Bacterial Growth

By nickwiecien

Bacterial biofilms are everywhere in nature and play an important role in many clinical, industrial, and ecological settings. Although much is known about the transcriptional regulatory networks that control biofilm formation in model bacteria such as Bacillus subtilis, very little is known about the role of metabolism in this process. To address this important knowledge gap, this study used a time-resolved analysis of the metabolic changes associated with bacterial biofilm development in B. subtilis by combining metabolomic, transcriptomic, and proteomic analyses. This report serves as a unique resource for future studies and will be relevant to future research in microbial physiology and metabolism. The full publication can be found here.

04 Dec 2019

Metandem, a free and online software for MS-based isobaric labeling metabolomics

By nickwiecien

Hao et al. (2019) recently published a paper in Analytica Chimica Acta detailing the utility of Metandem, a data analysis software which is aids in isobaric labeling-based metabolomics.

While mass spectrometry-based stable isotope labeling is advantageous compared to other methods of isotope labeling due to its multiplexing and accurate quantification capabilities, its data analysis requires specifically customized bioinformatic tools. However, Metandem, a free, unique and online software, can aid in the analysis of stable isotope labeling-based metabolomics data.

Metandem has a number of different features that assist in MS-based isobaric labeling, such as integrating feature extraction, metabolite quantification and identification, batch processing of multiple data files, online parameter optimization for custom datasets, data normalization and statistical analysis.

Metatandem is available free and online at http://metandem.com/web/. 

Graphical abstract for Metandem paper published by Hao et al in Analtica Chimica Acta demonstrating the software's utility in isobaric labeling, integrating feature extraction, and metabolite quantification.