- -

PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

RiuNet: Repositorio Institucional de la Universidad Politécnica de Valencia

Compartir/Enviar a

Citas

Estadísticas

  • Estadisticas de Uso

PFA toolbox: a MATLAB tool for Metabolic Flux Analysis

Mostrar el registro sencillo del ítem

Ficheros en el ítem

Thumbnail
Nombre: Bosque;Picó - PFA ...
Tamaño: 1012.Kb
Formato: PDF
Descripción: Versión editorial
Abrir
dc.contributor.author Morales, Yeimy es_ES
dc.contributor.author Bosque Chacón, Gabriel es_ES
dc.contributor.author Vehi, Josep es_ES
dc.contributor.author Picó Marco, Jesús Andrés es_ES
dc.contributor.author Llaneras, Francisco es_ES
dc.date.accessioned 2016-10-31T12:02:38Z
dc.date.available 2016-10-31T12:02:38Z
dc.date.issued 2016-07-11
dc.identifier.issn 1752-0509
dc.identifier.uri http://hdl.handle.net/10251/72995
dc.description.abstract Background: Metabolic Flux Analysis (MFA) is a methodology that has been successfully applied to estimate metabolic fluxes in living cells. However, traditional frameworks based on this approach have some limitations, particularly when measurements are scarce and imprecise. This is very common in industrial environments. The PFA Toolbox can be used to face those scenarios. Results: Here we present the PFA (Possibilistic Flux Analysis) Toolbox for MATLAB, which simplifies the use of Interval and Possibilistic Metabolic Flux Analysis. The main features of the PFA Toolbox are the following: (a) It provides reliable MFA estimations in scenarios where only a few fluxes can be measured or those available are imprecise. (b) It provides tools to easily plot the results as interval estimates or flux distributions. (c) It is composed of simple functions that MATLAB users can apply in flexible ways. (d) It includes a Graphical User Interface (GUI), which provides a visual representation of the measurements and their uncertainty. (e) It can use stoichiometric models in COBRA format. In addition, the PFA Toolbox includes a User s Guide with a thorough description of its functions and several examples. Conclusions: The PFA Toolbox for MATLAB is a freely available Toolbox that is able to perform Interval and Possibilistic MFA estimations. es_ES
dc.description.sponsorship This research has been partially supported by the Spanish Government (FEDER-CICYT: DPI 2014-55276-C5-1-R). Yeimy Morales is grateful for the BR Grants of the University of Girona (BR2012/26). Gabriel Bosque Chacon is recipient of a doctoral fellowship from the Spanish Government (BES-2012-053772). en_EN
dc.language Inglés es_ES
dc.publisher BioMed Central es_ES
dc.relation.ispartof BMC Systems Biology es_ES
dc.rights Reconocimiento (by) es_ES
dc.subject Metabolic Flux Analysis es_ES
dc.subject Interval MFA es_ES
dc.subject Possibilistic MFA es_ES
dc.subject Constraint-based modelling es_ES
dc.subject.classification INGENIERIA DE SISTEMAS Y AUTOMATICA es_ES
dc.title PFA toolbox: a MATLAB tool for Metabolic Flux Analysis es_ES
dc.type Artículo es_ES
dc.identifier.doi 10.1186/s12918-016-0284-1
dc.relation.projectID info:eu-repo/grantAgreement/UdG//BR2012%2F26/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//BES-2012-053772/ES/BES-2012-053772/ es_ES
dc.relation.projectID info:eu-repo/grantAgreement/MINECO//DPI2014-55276-C5-1-R/ES/BIOLOGIA SINTETICA PARA LA MEJORA EN BIOPRODUCCION: DISEÑO, OPTIMIZACION, MONITORIZACION Y CONTROL/ es_ES
dc.rights.accessRights Abierto es_ES
dc.contributor.affiliation Universitat Politècnica de València. Instituto Universitario de Automática e Informática Industrial - Institut Universitari d'Automàtica i Informàtica Industrial es_ES
dc.contributor.affiliation Universitat Politècnica de València. Escuela Técnica Superior de Ingenieros Industriales - Escola Tècnica Superior d'Enginyers Industrials es_ES
dc.description.bibliographicCitation Morales, Y.; Bosque Chacón, G.; Vehi, J.; Picó Marco, JA.; Llaneras, F. (2016). PFA toolbox: a MATLAB tool for Metabolic Flux Analysis. BMC Systems Biology. 10(46):1-10. https://doi.org/10.1186/s12918-016-0284-1 es_ES
dc.description.accrualMethod S es_ES
dc.relation.publisherversion http://dx.doi. org/10.1186/s12918-016-0284-1 es_ES
dc.description.upvformatpinicio 1 es_ES
dc.description.upvformatpfin 10 es_ES
dc.type.version info:eu-repo/semantics/publishedVersion es_ES
dc.description.volume 10 es_ES
dc.description.issue 46 es_ES
dc.relation.senia 316452 es_ES
dc.identifier.pmid 27401090 en_EN
dc.identifier.pmcid PMC4940746 en_EN
dc.contributor.funder Ministerio de Economía y Competitividad es_ES
dc.contributor.funder Universitat de Girona es_ES
dc.description.references Sauer U, Hatzimanikatis V, Bailey J, Hochuli M, Szyperski T, Wuethrich K. Metabolic fluxes in riboflavin-producing Bacillus subtilis. Nature biotechnology. 1997;15(5):448–52. es_ES
dc.description.references Wittmann C. Metabolic flux analysis using mass spectrometry. In: Tools and Applications of Biochemical Engineering Science. Berlin: Springer; 2002. p. 39–64. es_ES
dc.description.references Antoniewicz M. Methods and advances in metabolic flux analysis: a mini-review. J Ind Microbiol Biot. 2015;42(3):317–25. es_ES
dc.description.references Araúzo-Bravo MR, Shimizu JK. An improved method for statistical analysis of metabolic flux analysis using isotopomer-mapping matrices with analytical expressions. J Biotech. 2003;05:117–33. es_ES
dc.description.references Klamt S, Schuster S, Gilles D. Calculability analysis in underdetermined metabolic networks illustrated by a model of the central metabolism in purple nonsulfur bacteria. Biotechnol Bioeng. 2002;77(7):734–51. es_ES
dc.description.references Llaneras F. Interval and possibilistic methods for constraint-based metabolic models, PhD Thesis. Universidad Politécnica de Valencia: Departamento de Ingeniería de Sistemas y Automática; 2011. es_ES
dc.description.references Llaneras F, Picó J. An interval approach for dealing with flux distributions and elementary modes activity patterns. J Theor Biol. 2007;246(2):290–308. es_ES
dc.description.references Llaneras F, Sala A, Picó J. A possibilistic framework for constraint-based metabolic flux analysis. BMC Syst Biol. 2009;3(1):79. es_ES
dc.description.references Tortajada M, Llaneras F, Picó J. Validation of a constraint-based model of Pichia pastoris metabolism under data scarcity. BMC Syst Biol. 2010;4(1):115. es_ES
dc.description.references Llaneras F, Picó J. A procedure for the estimation over time of metabolic fluxes in scenarios where measurements are uncertain and/or insufficient. BMC Bioinformatics. 2007;8(1):421. es_ES
dc.description.references Iyer VV, Ovacik MA, Androulakis IP, Roth CM, Ierapetritou MG. Transcriptional and metabolic flux profiling of triadimefon effects on cultured hepatocytes. Toxicology and applied pharmacology. 2010;248(3):165–77. es_ES
dc.description.references Zamorano F, Wouwer A, Bastin G. Detailed metabolic flux analysis of an underdetermined network of CHO cells. J Biotechnol. 2010;150(4):497–508. es_ES
dc.description.references Iyer V, Yang H, Ierapetritou M, Roth C. Effects of glucose and insulin on HepG2‐C3A cell metabolism. Biotechnol Bioeng. 2010;107(2):347–56. es_ES
dc.description.references Iyer V, Androulakis I, Roth C, Ierapetritou M. Effects of Triadimefon on the Metabolism of Cultured Hepatocytes. In: BioInformatics and BioEngineering (BIBE), IEEE International Conference on. 2010. p. 118–23. es_ES
dc.description.references Orman MA, Arai K, Yarmush ML, Androulakis IP, Berthiaume F, Ierapetritou MG. Metabolic flux determination in perfused livers by mass balance analysis: effect of fasting. Biotechnology and bioengineering. 2010;107(5):825–35. es_ES
dc.description.references Hoppe A, Hoffmann S, Gerasch A, Gille C, Holzhütter H. FASIMU: flexible software for flux-balance computation series in large metabolic networks. BMC bioinformatics. 2011;12(1):28. es_ES
dc.description.references González J, Folch-Fortuny A, Llaneras F, Tortajada M, Picó J, Ferrer A. Metabolic flux understanding of Pichia pastoris grown on heterogenous culture media. Chemometr Intell Lab. 2014;134:89–99. es_ES
dc.description.references Morales Y, Tortajada M, Picó J, Vehí J, Llaneras F. Validation of an FBA model for Pichia pastoris in chemostat cultures. BMC System Biol. 2014;8(1):142. es_ES
dc.description.references Stephanopoulos GN, Aristidou AA, Nielsen J. Metabolic Engineering: Principles and Methodologies. San Diego, USA: Academic; 1998. es_ES
dc.description.references Heijden R, Romein B, Heijnen J, Hellinga C, Luyben K. Linear constraint relations in biochemical reaction systems: I & II. Biotech Bioeng. 1994;43(1):3–10. es_ES
dc.description.references Lofberg J. YALMIP: A toolbox for modeling and optimization in MATLAB. In: IEEE International Symposium on Computer Aided Control Systems Design. 2004. p. 284–9. es_ES
dc.description.references YALMIP Home Page [ http://users.isy.liu.se/johanl/yalmip/ ]. Accessed 11 May 2016. es_ES
dc.description.references IBM ILOG CPLEX- High-performance mathematical programming engine. [ http://www-01.ibm.com/software/commerce/optimization/cplex-optimizer/ ]. Accessed 11 May 2016. es_ES
dc.description.references GLPK (GNU Linear programming kit) [ http://www.gnu.org/software/glpk/ ]. Accessed 11 May 2016. es_ES
dc.description.references Orth D, Fleming M, Palsson B. Reconstruction and use of microbial metabolic networks: the core Escherichia coli metabolic model as an educational guide. EcoSal Plus. 2010;4:1. es_ES
dc.description.references Emmerling M, Dauner M, Ponti A, Fiaux J, Hochuli M, Szyperski T, Wüthrich K, Bailey J, Sauer U. Metabolic flux responses to pyruvate kinase knockout in Escherichia coli. Journal of bacteriology. 2002;184(1):152–64. es_ES
dc.description.references Orth J, Conrad T, Na J, Lerman J, Nam H, Feist A, Palsson B. A comprehensive genome‐scale reconstruction of Escherichia coli metabolism—2011. Molecular systems biology. 2011;7(1):535. es_ES
dc.description.references Bonarius H, Schmid G, Tramper J. Flux analysis of underdetermined metabolic networks: the quest for the missing constraints. Trends in Biotechnology. 1997;15(8):308–14. es_ES
dc.description.references Palsson BØ. Systems biology: properties of reconstructed networks. New York: Cambridge University Press; 2006. es_ES
dc.description.references Schilling C, Covert M, Famili I, Church G, Edwards J, Palsson B. Genome-scale metabolic model of Helicobacter pylori 26695. Journal of Bacteriology. 2002;184(16):4582–93. es_ES
dc.description.references Solà A, Jouhten P, Maaheimo H, Sánchez-Ferrando F, Szyperski T, Ferrer P. Metabolic flux profiling of Pichia pastoris grown on glycerol/methanol mixtures in chemostat cultures at low and high dilution rates. Microbiol. 2007;153:281–90. es_ES
dc.description.references Solà A. Estudi del metabolisme central del carboni de Pichia pastoris, PhD Thesis. Universitat Autònoma de Barceloana: Escola Tècnica Superior d’Enginyeria; 2004. es_ES
dc.description.references Jungo C, Rerat C, Marison IW, von Stockar U. Quantitative characterization of the regulation of the synthesis of alcohol oxidase and of the expression of recombinant avidin in a Pichia pastoris Mut + strain. Enzyme Microb Technol. 2006;39:936–44. es_ES
dc.description.references Tortajada M. Process development for the obtention and use of recombinant glycosidases: expression, modelling and immobilization, PhD Thesis. Universidad Politécnica de Valencia: Departamento de Ingeniería de Sistemas y Automática; 2012. es_ES
dc.description.references Jordà J, de Jesus SS, Peltier S, Ferrer P, Albiol J. Metabolic flux analysis of recombinant Pichia pastoris growing on different glycerol/methanol mixtures by iterative fitting of NMR-derived 13C-labelling data from proteinogenic amino acids. New Biotecnol. 2014;31(1):120–32. es_ES


Este ítem aparece en la(s) siguiente(s) colección(ones)

Mostrar el registro sencillo del ítem