Fast Sampling of the Cellular Metabolome View Full Text


Ontology type: schema:Chapter     


Chapter Info

DATE

2012

AUTHORS

Walter M. Van Gulik , Andre B. Canelas , Hilal Taymaz-Nikerel , Rutger D. Douma , Lodewijk P. de Jonge , Joseph J. Heijnen

ABSTRACT

Obtaining meaningful snapshots of the metabolome of microorganisms requires rapid sampling and immediate quenching of all metabolic activity, to prevent any changes in metabolite levels after sampling. Furthermore, a suitable extraction method is required ensuring complete extraction of metabolites from the cells and inactivation of enzymatic activity, with minimal degradation of labile compounds. Finally a sensitive, high-throughput analysis platform is needed to quantify a large number of metabolites in a small amount of sample. An issue which has often been overlooked in microbial metabolomics is the fact that many intracellular metabolites are also present in significant amounts outside the cells, and may interfere with the endometabolome measurements. Attempts to remove the extracellular metabolites with dedicated quenching methods often induce release of intracellular metabolites into the quenching solution. For eukaryotic microorganisms, leakage can be minimized by adaptation of the quenching method. For prokaryotic cells this had not yet been accomplished, so the application of a differential method whereby metabolites are measured in the culture supernatant as well as in total broth samples, to calculate the intracellular levels by subtraction, seems to be the most suitable approach. Here we present an overview of different sampling, quenching, and extraction methods developed for microbial metabolomics, described in the literature. Detailed protocols are provided for rapid sampling, quenching, and extraction for measurement of metabolites in total broth samples, washed cell samples and supernatant, to be applied for quantitative metabolomics of both eukaryotic and prokaryotic microorganisms. More... »

PAGES

279-306

Book

TITLE

Microbial Systems Biology

ISBN

978-1-61779-826-9
978-1-61779-827-6

Author Affiliations

Identifiers

URI

http://scigraph.springernature.com/pub.10.1007/978-1-61779-827-6_10

DOI

http://dx.doi.org/10.1007/978-1-61779-827-6_10

DIMENSIONS

https://app.dimensions.ai/details/publication/pub.1017887011

PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/22639217


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Download the RDF metadata as:  json-ld nt turtle xml License info

HOW TO GET THIS DATA PROGRAMMATICALLY:

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curl -H 'Accept: application/ld+json' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-827-6_10'

N-Triples is a line-based linked data format ideal for batch operations.

curl -H 'Accept: application/n-triples' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-827-6_10'

Turtle is a human-readable linked data format.

curl -H 'Accept: text/turtle' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-827-6_10'

RDF/XML is a standard XML format for linked data.

curl -H 'Accept: application/rdf+xml' 'https://scigraph.springernature.com/pub.10.1007/978-1-61779-827-6_10'


 

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