Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos
ilustraciones, diagramas
- Autores:
-
Vásquez Restrepo, Andrés
- Tipo de recurso:
- Fecha de publicación:
- 2022
- Institución:
- Universidad Nacional de Colombia
- Repositorio:
- Universidad Nacional de Colombia
- Idioma:
- spa
- OAI Identifier:
- oai:repositorio.unal.edu.co:unal/83418
- Palabra clave:
- 570 - Biología::572 - Bioquímica
Biotechnology
Electrochemistry
Biochemistry
Electroquímica
Biotecnología
Bioquímica
Omics
In silico
Ingeniería metabólica
Diseño Racional de Bioprocesos
Biotermodinámica
Metabolic Engineering
Rational Design of Bioprocesses
Biothermodynamics
- Rights
- openAccess
- License
- Atribución-NoComercial 4.0 Internacional
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| dc.title.spa.fl_str_mv |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos |
| dc.title.translated.eng.fl_str_mv |
In-silico exploration of Electro-fermentation strategies in the Rational Design of Bioprocesses |
| title |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos |
| spellingShingle |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos 570 - Biología::572 - Bioquímica Biotechnology Electrochemistry Biochemistry Electroquímica Biotecnología Bioquímica Omics In silico Ingeniería metabólica Diseño Racional de Bioprocesos Biotermodinámica Metabolic Engineering Rational Design of Bioprocesses Biothermodynamics |
| title_short |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos |
| title_full |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos |
| title_fullStr |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos |
| title_full_unstemmed |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos |
| title_sort |
Exploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesos |
| dc.creator.fl_str_mv |
Vásquez Restrepo, Andrés |
| dc.contributor.advisor.none.fl_str_mv |
SUAREZ-MENDEZ, CAMILO |
| dc.contributor.author.none.fl_str_mv |
Vásquez Restrepo, Andrés |
| dc.contributor.researchgroup.spa.fl_str_mv |
Bioprocesos y Flujos Reactivos |
| dc.contributor.orcid.spa.fl_str_mv |
Vasquez-Restrepo, Andres [0000-0001-9627-1005] Suárez Méndez, Camilo[0000-0002-5345-9662] |
| dc.contributor.cvlac.spa.fl_str_mv |
https://scienti.colciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=0000122302 |
| dc.subject.ddc.spa.fl_str_mv |
570 - Biología::572 - Bioquímica |
| topic |
570 - Biología::572 - Bioquímica Biotechnology Electrochemistry Biochemistry Electroquímica Biotecnología Bioquímica Omics In silico Ingeniería metabólica Diseño Racional de Bioprocesos Biotermodinámica Metabolic Engineering Rational Design of Bioprocesses Biothermodynamics |
| dc.subject.lemb.eng.fl_str_mv |
Biotechnology Electrochemistry Biochemistry |
| dc.subject.lemb.spa.fl_str_mv |
Electroquímica Biotecnología Bioquímica |
| dc.subject.proposal.spa.fl_str_mv |
Omics In silico Ingeniería metabólica Diseño Racional de Bioprocesos Biotermodinámica |
| dc.subject.proposal.eng.fl_str_mv |
Metabolic Engineering Rational Design of Bioprocesses Biothermodynamics |
| description |
ilustraciones, diagramas |
| publishDate |
2022 |
| dc.date.issued.none.fl_str_mv |
2022 |
| dc.date.accessioned.none.fl_str_mv |
2023-02-10T16:33:23Z |
| dc.date.available.none.fl_str_mv |
2023-02-10T16:33:23Z |
| dc.type.spa.fl_str_mv |
Trabajo de grado - Maestría |
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info:eu-repo/semantics/masterThesis |
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info:eu-repo/semantics/acceptedVersion |
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Text |
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http://purl.org/redcol/resource_type/TM |
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acceptedVersion |
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https://repositorio.unal.edu.co/handle/unal/83418 |
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Universidad Nacional de Colombia |
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Repositorio Institucional Universidad Nacional de Colombia |
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https://repositorio.unal.edu.co/ |
| url |
https://repositorio.unal.edu.co/handle/unal/83418 https://repositorio.unal.edu.co/ |
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Universidad Nacional de Colombia Repositorio Institucional Universidad Nacional de Colombia |
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spa |
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spa |
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RedCol LaReferencia |
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Harnisch, “Modeling microbial electrosynthesis,” in Advances in Biochemical Engineering/Biotechnology, vol. 167, Springer Science and Business Media Deutschland GmbH, 2019, pp. 273–325. H. Rismani-Yazdi, A. D. Christy, S. M. Carver, Z. Yu, B. A. Dehority, and O. H. Tuovinen, “Effect of external resistance on bacterial diversity and metabolism in cellulose-fed microbial fuel cells,” Bioresour. Technol., vol. 102, no. 1, pp. 278–283, 2011, doi: 10.1016/j.biortech.2010.05.012. F. Kracke and J. O. Krömer, “Identifying target processes for microbial electrosynthesis by elementary mode analysis,” 2014, doi: 10.1186/s12859-014-0410-2. F. Kracke, B. Lai, S. Yu, and J. O. Krömer, “Balancing cellular redox metabolism in microbial electrosynthesis and electro fermentation – A chance for metabolic engineering,” Metabolic Engineering, vol. 45. Academic Press Inc., pp. 109–120, Jan. 01, 2018, doi: 10.1016/j.ymben.2017.12.003. T. D. 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Sturm-Richter et al., “Unbalanced fermentation of glycerol in Escherichia coli via heterologous production of an electron transport chain and electrode interaction in microbial electrochemical cells,” Bioresour. Technol., vol. 186, pp. 89–96, Jun. 2015, doi: 10.1016/j.biortech.2015.02.116. J. P. O’Brien and N. S. Malvankar, “A Simple and Low-Cost Procedure for Growing Geobacter sulfurreducens Cell Cultures and Biofilms in Bioelectrochemical Systems,” Curr. Protoc. Microbiol., vol. 43, no. 1, p. A.4K.1-A.4K.27, Nov. 2016, doi: 10.1002/CPMC.20. C. Koch, B. Korth, and F. Harnisch, “Microbial ecology-based engineering of Microbial Electrochemical Technologies,” Microb. Biotechnol., vol. 11, no. 1, pp. 22–38, Jan. 2018, doi: 10.1111/1751-7915.12802. M. Kanehisa, Y. Sato, and M. Kawashima, “KEGG mapping tools for uncovering hidden features in biological data,” Protein Sci., vol. 31, no. 1, pp. 47–53, Jan. 2022, doi: 10.1002/PRO.4172. J. M. Flynn, D. E. Ross, K. A. Hunt, D. R. Bond, and J. A. Gralnick, “Enabling unbalanced fermentations by using engineered electrode- interfaced bacteria,” MBio, vol. 1, no. 5, Nov. 2010, doi: 10.1128/mBio.00190-10. J. M. Monk et al., “Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments,” Proc. Natl. Acad. Sci. U. S. A., vol. 110, no. 50, pp. 20338–20343, Dec. 2013, doi: 10.1073/PNAS.1307797110/-/DCSUPPLEMENTAL. F. C. Neidhardt, “Chemical Composition of Escherichia Coli,” Escherichia coli Salmonella typhimurium - Cell. Mol. Biol., p. 2822, 1987, [Online]. Available: https://www.journals.uchicago.edu/doi/abs/10.1086/416059. J. Pramanik and J. D. Keasling, “Stoichiometric model of Escherichia coli metabolism: Incorporation of growth-rate dependent biomass composition and mechanistic energy requirements,” Biotechnol. Bioeng., vol. 56, no. 4, pp. 398–421, 1997, doi: 10.1002/(SICI)1097-0290(19971120)56:4<398::AID-BIT6>3.0.CO;2-J. J. A. Roels, “Application of Macroscopic Principles To Microbial Metabolism,” Ann. N. Y. Acad. Sci., vol. 369, no. 1, pp. 113–134, 1981, doi: 10.1111/j.1749-6632.1981.tb14182.x. F. Kracke, B. Virdis, P. V. Bernhardt, K. Rabaey, and J. O. Krömer, “Redox dependent metabolic shift in Clostridium autoethanogenum by extracellular electron supply,” Biotechnol. Biofuels, vol. 9, no. 1, pp. 1–12, 2016, doi: 10.1186/s13068-016-0663-2. |
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Atribución-NoComercial 4.0 Internacionalhttp://creativecommons.org/licenses/by-nc/4.0/info:eu-repo/semantics/openAccesshttp://purl.org/coar/access_right/c_abf2SUAREZ-MENDEZ, CAMILO0cb894551eb9c1f9737a27b5a0b26d87600Vásquez Restrepo, Andrés3c1b08f3bb6101be643086b4f7ed2c3d600Bioprocesos y Flujos ReactivosVasquez-Restrepo, Andres [0000-0001-9627-1005]Suárez Méndez, Camilo[0000-0002-5345-9662]https://scienti.colciencias.gov.co/cvlac/visualizador/generarCurriculoCv.do?cod_rh=00001223022023-02-10T16:33:23Z2023-02-10T16:33:23Z2022https://repositorio.unal.edu.co/handle/unal/83418Universidad Nacional de ColombiaRepositorio Institucional Universidad Nacional de Colombiahttps://repositorio.unal.edu.co/ilustraciones, diagramasLa electro-fermentación es una estrategia emergente para optimizar los bioprocesos al regular el balance redox intracelular y redireccionar los flujos metabólicos. En el presente trabajo se evaluó in silico la electro-fermentación desde el marco del diseño racional de bioprocesos para determinar su efecto en el aprovechamiento de la energía biológicamente disponible y los rendimientos del proceso. Para lo cual, se desarrolló una metodología que permitió estimar sus costos energéticos asociados y evaluar su capacidad de redireccionamiento metabólico. Se definieron un conjunto de semirreacciones que permitieron utilizar los principios de la electroquímica para establecer los requerimientos energéticos del proceso, junto con su modelo de caja negra. Se encontró que la energía libre de Gibbs de reacción depende del voltaje aplicado y el potencial de reducción de la molécula aceptora interna de electrones. Además, se planteó un modelo metabólico que incluyó el transporte extracelular de electrones y permitió evidenciar los diferentes cambios metabólicos al cambiar el balance redox a través de la interacción con el electrodo. Finalmente, se evaluaron diferentes casos de estudio para evidenciar el desempeño de la metodología desarrollada, en donde se logró solucionar déficits de ATP y electrones a expensas de una pequeña desviación de carbonos hacia subproductos debido a la generación de un desbalance redox en el metabolismo celular. La presente metodología representa un primer intento de una estimación in silico de los requerimientos de corriente eléctrica y voltaje asociados a una electro-fermentación a partir de fundamentos teóricos. (Texto tomado de la fuente)Electro-fermentation is a novel strategy for optimizing bioprocesses in which the intracellular redox balance is regulated to redirect the carbon metabolic flux towards a desired product. In this work, an in-silico evaluation of the electro-fermentation has been made within the frame of a methodology referred to as Rational Design of Bioprocesses to evaluate its effects on microbial bioenergetics and process performance. Here, a new methodology is proposed for estimating the associated Gibbs energy costs, the development of a black-box model and the evaluation of its capacity to redirect metabolic fluxes. A set of semi reactions are used to describe the interactions between the electrode and the microbe, where the Gibbs energy involved in the electro-fermentation process is associated to the electrode’s poised voltage and the standard reduction potential of the internal electron acceptor. Besides, a new metabolic model is developed incorporating a set of reactions for the extracellular electron transfer mechanism. It has been proven that metabolic changes occur by an unbalanced NADH pool generated by the interaction of the microbe with a poised electrode. Finally, both thermodynamic and metabolic models are used in different study cases to evaluate the performance of the complete developed framework for electro-fermentations, where it has been proven that it can be used to solve ATP deficits in metabolic networks. To my knowledge, it is the first attempt of an in-silico based theorical framework to describe the energy, current and voltage associated with electro-fermentations.MaestríaMagister en Ciencias - BiotecnologíaDiseño Racional de BioprocesosÁrea Curricular de Bioctecnología210 páginasapplication/pdfspaUniversidad Nacional de ColombiaMedellín - Ciencias - Maestría en Ciencias - BiotecnologíaFacultad de CienciasMedellín, ColombiaUniversidad Nacional de Colombia - Sede Medellín570 - Biología::572 - BioquímicaBiotechnologyElectrochemistryBiochemistryElectroquímicaBiotecnologíaBioquímicaOmicsIn silicoIngeniería metabólicaDiseño Racional de BioprocesosBiotermodinámicaMetabolic EngineeringRational Design of BioprocessesBiothermodynamicsExploración in silico de estrategias de electro-fermentación en el diseño racional de bioprocesosIn-silico exploration of Electro-fermentation strategies in the Rational Design of BioprocessesTrabajo de grado - Maestríainfo:eu-repo/semantics/masterThesisinfo:eu-repo/semantics/acceptedVersionTexthttp://purl.org/redcol/resource_type/TMRedColLaReferenciaL. 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Biofuels, vol. 9, no. 1, pp. 1–12, 2016, doi: 10.1186/s13068-016-0663-2.EstudiantesInvestigadoresORIGINAL1017236136_2022.pdf1017236136_2022.pdfTesis de Maestría en Ciencias - Biotecnologíaapplication/pdf2136850https://repositorio.unal.edu.co/bitstream/unal/83418/2/1017236136_2022.pdf6245516e50c51bec90a88cca0c814944MD52LICENSElicense.txtlicense.txttext/plain; charset=utf-85879https://repositorio.unal.edu.co/bitstream/unal/83418/1/license.txteb34b1cf90b7e1103fc9dfd26be24b4aMD51unal/83418oai:repositorio.unal.edu.co:unal/834182023-02-10 11:37:53.286Repositorio Institucional Universidad Nacional de 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