Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks

Nookaew, Intawat; Meechai, Asawin; Thammarongtham, Chinae; Laoteng, Kobkul; Ruanglek, Vasimon; Cheevadhanarak, Supapon; Nielsen, Jens; Bhumiratana, Sakarindr

doi:10.1002/bit.21339

Cited by 32 publications

(25 citation statements)

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“…The correlation of appropriate weighting factors with EMs or with extreme pathways, respectively, to achieve a successful combination which describes a physiological state or its changes caused by perturbations of cultivation conditions, is still a challenging task. Recently, several reports on these procedures were published: the concept of the a-spectrum (Wiback et al , 2004, Moore-Penrose generalized inverse (Poolman et al 2004), carbon source uptake rates combined with efficient biomass and energy producing EFMs (Carlson and Srienc 2004a, b), identification of the most dominant subset of biologically active EMs combined with kinetic modelling (Schwartz and Kanehisa 2005;2006), the classical thermodynamics approach ), the open system in the near equilibrium steady state (Qian and Beard 2005;Qian et al 2003), as well as the flux regulation coefficients with experimentally determined exchange fluxes (Nookaew et al 2007) and quadratic programming approach (Wang et al 2007). …”

Section: Metabolic Pathway Analysis (Mpa)mentioning

confidence: 99%

Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies

Horvat

Koller

Braunegg

2015

World J Microbiol Biotechnol

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A review of the use of elementary flux modes (EFMs) and their applications in metabolic engineering covered with yield space analysis (YSA) is presented. EFMs are an invaluable tool in mathematical modeling of biochemical processes. They are described from their inception in 1994, followed by various improvements of their computation in later years. YSA constitutes another precious tool for metabolic network modeling, and is presented in details along with EFMs in this article. The application of these techniques is discussed for several case studies of metabolic network modeling provided in respective original articles. The article is concluded by some case studies in which the application of EFMs and YSA turned out to be most useful, such as the analysis of intracellular polyhydroxyalkanoate (PHA) formation and consumption in Cupriavidus necator, including the constraint-based description of the steady-state flux cone of the strain's metabolic network, the profound analysis of a continuous five-stage bioreactor cascade for PHA production by C. necator using EFMs and, finally, the study of metabolic fluxes in the metabolic network of C. necator cultivated on glycerol.

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Section: Metabolic Pathway Analysis (Mpa)mentioning

confidence: 99%

Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies

Horvat

Koller

Braunegg

2015

World J Microbiol Biotechnol

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“…In the work of Nookaew et al [39], a new technique for the determination of fluxes has been developed. The convex properties of EFMs are used to calculate a weighing factor for each EFM corresponding to an appropriate fractional operation of this mode within the complete set of EFMs.…”

Section: Elementary Flux Modes and Extreme Pathwaysmentioning

confidence: 99%

“…EFMs will be finally computed, thanks to Metatool [34], and the deduced macro-reactions will be derived into differential equations [32]. FRCs [39] could also be computed for a cross-validation of the MFA.…”

Section: Mathematical and Computer Modelling Of Dynamical Systems 549mentioning

confidence: 99%

Two modelling approaches of winemaking: first principle and metabolic engineering

Charnomordic

David

Dochain

et al. 2010

Mathematical and Computer Modelling of Dynamical Systems

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In this article, two modelling approaches are proposed for winemaking fermentations. The first one is largely based on the first principle modelling approach and considers the main yeast physiological mechanisms. The model accurately predicts the fermentation kinetics of more than 80% of a large number of experiments performed with 20 wine yeast strains, 69 musts and different fermentation conditions. Thanks to the wide domain of validity of the model, a simulator based on this model coupled to a thermal model was developed to help winemakers to optimize tank management. It predicts the end of the fermentation and changes in the rate of fermentation but furthermore includes an optimization module based on fuzzy logic which allows, via temperature profiles and nitrogen addition strategies, to decrease the duration of fermentation and the energy requirements at winery scale according to user specifications. The objective of the second modelling approach is the development of a mathematical model of the fermentation process including some minority by-products known as characteristic flavour compounds. It refers to metabolic engineering and accounts for the intracellular behaviour of the yeast Saccharomyces cerevisiae by using approaches like the metabolic flux analysis (MFA) and the elementary flux modes (EFMs). A state of the art describes the application of these methods in the restrained field of winemaking/ fermentation conditions and underlines the potential of such approaches.

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“…To face this situation, one could choose one flux vector among those that are compatible with the measurements. For instance, Nookaew et al have proposed to estimate the intracellular fluxes based on the assumption that cells are likely to use as many pathways as possible to maintain robustness and redundancy (Nookaew, 2007). Related hypotheses have been formulated using the concept of elementary modes (Poolman, 2004;Schwartz, 2006).…”

Section: Introductionmentioning

confidence: 99%

“…These constraint-based models are often build upon large, or genome-scale, networks of well-characterised organisms such as E. coli, S. cerevisiae, or P. putida, (Feist, 2007;Nogales, 2008) but also in simpler networks that consider only a few key metabolites Teixeira, 2007;Nookaew, 2007).…”

Section: Introductionmentioning

confidence: 99%

Interval and Possibilistic Methods for Constraint-Based Metabolic Models

Estrada¹

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In the following site the reader will find updated information regarding this thesis. This includes corrections and clarifications, connections with future works, publications, software and tools, etc.http://science.ensilicio.com/Thesis/Thesis.html AgradecimientosLa tesis doctoral es un viaje emocionante, exigente y no exento de riesgos. Por suerte, resulta mucho mejor, más sencillo y más divertido, cuando uno tiene una lista de agradecimientos tan extensa como la mía.Estoy en deuda con mi director, Jesús Picó, por darme la oportunidad de trabajar en lo que me gusta, por descubrirme un tema fascinante y por dirigirme sabiamente en el desarrollo de esta tesis. También con mis supervisores durante mis estancias en el extranjero, Georges Bastin y Vassily Hatzimanikatis, porque me permitieron aprender de su trabajo, conocer sus instituciones y explorar dos países.Le agradezco a Antonio Sala que se acercase un buen día con una propuesta para colaborar (haciendo así fructíferas las reuniones en la biblioteca); y a Marta Tortajada que fuese mi coautora en varias ocasiones y que sea una de las personas cuyas ideas más me han ayudado. He aprendido mil cosas de otras personas -profesores, compañeros, colegas, revisores, etc.-y a todos les estoy agradecido.A los compañeros que encontré camino al doctorado les agradezco, sobretodo, que hicieran mi trabajo divertido. Agradezco cada café y cada conversación. Mención especial merecen mis principales compañeros de viaje, Pepe y Sergio, por su camaradería en el trabajo y en la vida.Es probable que sin el apoyo de otras personas no hubiese terminado esta tesis... y es seguro que de haberlo hecho sería irrelevante. A mi familia -Juan, María, Juan-les agradezco que sean mi refugio, porque la existencia de ese «lugar» me permite el lujo de ser temerario. A mis amigos en la vecindad les agradezco su interés por las victorias de cada día; y tanto a ellos como al resto, les doy las gracias por creer incondicionalmente que lo que hacía, fuese lo que fuese, era digno de admirar. Mi deuda es especial con Lucia porque ella fue la recompensa en los días de trabajo y sacrificio.Por último, y por encima de todo, quiero agradecer a mis padres todo lo que hicieron y el modo preciso en que lo hicieron. Sé que eso excede el ámbito de esta tesis, pero este párrafo es un buen lugar para mostrarles mi gratitud. Gracias. AbstractThis thesis is devoted to the study and application of constraint-based metabolic models. The objective was to find simple ways to handle the difficulties that arise in practice due to uncertainty (knowledge is incomplete, there is a lack of measurable variables, and those available are imprecise). With this purpose, tools have been developed to model, analyse, estimate and predict the metabolic behaviour of cells.The document is structured in three parts. First, related literature is revised and summarised. This results in a unified perspective of several methodologies that use constraint-based representations of the cell metabolism. Three outstanding methods are discussed i...

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Identification of flux regulation coefficients from elementary flux modes: A systems biology tool for analysis of metabolic networks

Cited by 32 publications

References 42 publications

Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies

Recent advances in elementary flux modes and yield space analysis as useful tools in metabolic network studies

Two modelling approaches of winemaking: first principle and metabolic engineering

Interval and Possibilistic Methods for Constraint-Based Metabolic Models

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