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A systems biology approach identifies the biochemical mechanisms regulating monoterpenoid essential oil composition in peppermint
- Rigoberto Ríos-Estepa, G. Turner, James M. Lee, R. Croteau, B. M. Lange
- Biology, MedicineProceedings of the National Academy of Sciences
- 26 February 2008
The development of a kinetic mathematical model that accurately simulates the developmental patterns of monoterpenoid essential oil accumulation in peppermint was used to evaluate the biochemical processes underlying experimentally determined changes in the monoterpene pathway under low ambient-light intensities.
Experimental and mathematical approaches to modeling plant metabolic networks.
It is argued that iterative cycles of (dry) mathematical modeling and (wet) laboratory testing will become increasingly important for simulating the distribution of flux in plant metabolic networks and deriving rational experimental designs for metabolic engineering efforts.
Mathematical Modeling-Guided Evaluation of Biochemical, Developmental, Environmental, and Genotypic Determinants of Essential Oil Composition and Yield in Peppermint Leaves1[W][OA]
- Rigoberto Ríos-Estepa, I. Lange, James M. Lee, B. M. Lange
- Biology, MedicinePlant Physiology
- 10 February 2010
Simulated and measured essential oil profiles were in very good agreement, indicating that modeling is a valuable tool for guiding metabolic engineering efforts aimed at improving essential oil quality and quantity.
Comparison of process technologies for chitosan production from shrimp shell waste: A techno-economic approach using Aspen Plus®
Techno-economic analyses for two different processing methods for chitosan production from shrimp shell waste were performed. Experimental lab-scale data that included the shrimp shell waste…
Kinetic modeling of plant metabolism and its predictive power: peppermint essential oil biosynthesis as an example.
This article describes a kinetic mathematical model of peppermint essential oil biosynthesis, a pathway that has been studied extensively for more than two decades and provides step-by-step instructions on how to run simulations of dynamic changes in pathway metabolites concentrations.
Metabolic adaptation of two in silico mutants of Mycobacterium tuberculosis during infection
- Víctor A López-Agudelo, A. Baena, H. Ramirez-Malule, Silvia Ochoa, L. Barrera, Rigoberto Ríos-Estepa
- Biology, MedicineBMC Systems Biology
- 21 November 2017
This study demonstrates the potential application of genome-scale modeling, flux balance analysis (FBA), phenotypic phase plane (PhPP) analysis and shadow pricing to generate valuable insights about Mtb metabolic reprogramming in the context of human granulomas.
An enhanced genome-scale metabolic reconstruction of Streptomyces clavuligerus identifies novel strain improvement strategies
- León F. Toro, Laura Pinilla, C. Avignone-Rossa, Rigoberto Ríos-Estepa
- Chemistry, MedicineBioprocess and Biosystems Engineering
- 5 February 2018
A genome-scale metabolic model of Streptomyces clavuligerus was expanded and updated and a strain design was carried out to identify candidate genes to be overexpressed or knocked out so as to maximize antibiotic biosynthesis.
Streptomyces clavuligerus shows a strong association between TCA cycle intermediate accumulation and clavulanic acid biosynthesis
- H. Ramirez-Malule, S. Junne, M. Nicolas Cruz-Bournazou, P. Neubauer, Rigoberto Ríos-Estepa
- Chemistry, MedicineApplied Microbiology and Biotechnology
- 9 March 2018
A strong association of succinate, oxaloacetate, malate, and acetate accumulation with CA production in S. clavuligerus was observed, and flux balance analysis (FBA) was used to describe the carbon flux distribution in the network.
Comparative Transcriptome Analysis of Streptomyces Clavuligerus in Response to Favorable and Restrictive Nutritional Conditions
- Laura Pinilla, León F. Toro, E. Laing, J. Alzate, Rigoberto Ríos-Estepa
- Medicine, BiologyAntibiotics
- 19 July 2019
The up-regulated expression of many regulatory and biosynthetic CA genes was positively associated with the favorable complex media condition along with pleiotropic regulators, including proteases and some genes whose biological function have not been previously reported.
Streptomyces clavuligerus strain selection for clavulanic acid biosynthesis: a study based on culture composition effects and statistical analysis
- Laura Pinilla, León F. Toro, C. Avignone-Rossa, M. Peñuela, Rigoberto Ríos-Estepa
- 1 April 2018
The clinical and industrial importance of clavulanic acid (CA) promotes the search for novel strategies to boost productivity at lower costs. In this contribution, the production of CA was evaluated…