Planning optimal measurements of isotopomer distributions for estimation of metabolic fluxes

Bioinformatics
Ari RantanenEsko Ukkonen

Abstract

Flux estimation using isotopomer information of metabolites is currently the most reliable method to obtain quantitative estimates of the activity of metabolic pathways. However, the development of isotopomer measurement techniques for intermediate metabolites is a demanding task. Careful planning of isotopomer measurements is thus needed to maximize the available flux information while minimizing the experimental effort. In this paper we study the question of finding the smallest subset of metabolites to measure that ensure the same level of isotopomer information as the measurement of every metabolite in the metabolic network. We study the computational complexity of this optimization problem in the case of the so-called positional enrichment data, give methods for obtaining exact and fast approximate solutions, and evaluate empirically the efficacy of the proposed methods by analyzing a metabolic network that models the central carbon metabolism of Saccharomyces cerevisiae.

References

Apr 18, 1998·European Journal of Biochemistry·B D Follstad, G Stephanopoulos
Aug 26, 1998·Quarterly Reviews of Biophysics·T Szyperski
Apr 1, 1999·Biotechnology and Bioengineering·C Wittmann, E Heinzle
Jul 8, 1999·Proceedings of the National Academy of Sciences of the United States of America·J ShenD L Rothman
Nov 24, 1999·Biotechnology and Bioengineering·M MöllneyA A de Graaf
Jul 20, 2001·Metabolic Engineering·W WiechertA A de Graaf
Aug 9, 2001·Biotechnology and Bioengineering·W A van WindenJ Grievink
Sep 21, 2002·Molecular Biology Reports·Steffen Klamt, Stefan Schuster
Apr 25, 2003·Mathematical Biosciences·Nicole Isermann, Wolfgang Wiechert
Dec 4, 2003·Journal of Bacteriology·Jens Nielsen
Jun 9, 2004·European Journal of Biochemistry·Aina SolàThomas Szyperski
Jul 19, 2008·Biotechnology and Bioengineering·K SchmidtJ Villadsen

❮ Previous
Next ❯

Citations

Dec 13, 2007·Bioprocess and Biosystems Engineering·P DrosteW Wiechert
May 30, 2009·Nature Protocols·Nicola ZamboniUwe Sauer
Jan 8, 2011·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Markus HeinonenJuho Rousu
Aug 31, 2007·BMC Bioinformatics·Michael WeitzelKatharina Nöh
May 5, 2009·Microbial Cell Factories·Lake-Ee QuekJens O Krömer
Jul 23, 2009·Journal of Biotechnology·Christian M MetalloGregory Stephanopoulos
Jun 17, 2008·Biotechnology and Bioengineering·YoungJung ChangCostas D Maranas
Mar 5, 2011·BMC Bioinformatics·Che-Wei ChangMasanori Arita
Mar 5, 2013·Current Opinion in Biotechnology·Maciek R Antoniewicz
Sep 27, 2016·Metabolic Engineering·Ziwei Dai, Jason W Locasale
Nov 15, 2006·Molecular Systems Biology·Uwe Sauer
May 24, 2014·The European Physical Journal. E, Soft Matter·Ping Wang, Xiaojing Zheng
Mar 5, 2013·Journal of Cheminformatics·Kerstin ScheubertSebastian Böcker
Jul 10, 2021·Frontiers in Bioengineering and Biotechnology·Martin BeyßKatharina Nöh

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.