Teaching cellular metabolism using metabolic model simulations

Author(s)

Chaves, Gabriel Luz ; Batista, Raquel Salgado ; Cunha, Josivan de Sousa ; Altmann, Daniel Lossa ; da Silva, Adilson Jose

• Document type: Journal article
• Source: EDUCATION FOR CHEMICAL ENGINEERS; v. 38, p. 13-pg., 2022-01-01.

Abstract

Teaching biology contents to chemical engineers is usually a challenging task, as it generally does not fit well to the quantitative approach with which engineering students are familiar. Here, we show that quantitative aspects of cellular metabolism can be explored using simulation tools, contributing to the engagement of students regarding this topic. Using OptFlux, an open-source software tool developed for metabolic engineering research, the students simulated the behavior of Escherichia coli and Saccharomyces cerevisiae cells under different environmental conditions. Exploring the user-friendly features of OptFlux, we present a set of four simulation tasks where the students are encouraged to discuss fundamental metabolic pathways such as glycolysis and the TCA cycle, the effect of genetic modifications on carbon flux redistribution through the metabolic network, and other important aspects of cell metabolism. The responses of the students to a questionnaire regarding the suitability of using OptFlux as an educational tool showed that their overall opinion was highly positive. Most students had no difficulties using the software and believed that the proposed exercises using OptFlux constituted a good strategy for teaching and reviewing cell metabolism concepts. Given these results, we believe that this alternative approach is a useful methodology for engaging students and facilitating the teaching of cellular metabolism to chemical engineers. (AU)

• FAPESP's process: 19/07902-6 - Development of a microbial cell factory for 3-hydroxypropionic production
• Grantee: Gabriel Luz Chaves
• Support Opportunities: Scholarships in Brazil - Master
• FAPESP's process: 19/09332-2 - Optimization of the aromatic compounds pathway in Escherichia coli for phenazines production
• Grantee: Daniel Lossa Altmann
• Support Opportunities: Scholarships in Brazil - Scientific Initiation