Enhancing genome-scale metabolic models with kinetic data: resolving growth and citramalate production trade-offs in Escherichia coli
Lay summary A common way to simulate metabolism in an organism is by metabolic models – mathematical equations that describe the dynamics of chemical reactions. Genome-scale constraint-based metabolic models account for most reactions that can occur in a cell and can be used to predict how much a genetically engineered microbe can produce an industrially relevant compound.
12 Jul 2025
Single-cell metabolic oscillations are pervasive and may alleviate a proteome constraint
Lay summary Biological rhythms are essential to controlling the function of living organisms. One such example is the metabolic cycle in budding yeast, which consists of cycling levels of metabolites, RNA transcripts, and oxygen consumption over time. Most studies on this cycle have been performed with chemostats, in batch-cultures. Though there are more recent studies that image cells individually, it is unclear how to reconcile finding from the two types of experiments.
26 Nov 2024
PhD Project
My PhD project was conducted under the joint supervision of Dr Diego Oyarzún (computational) and Prof Peter Swain (laboratory & computational), at the University of Edinburgh. My project examined the metabolic cycle in budding yeast. This yeast metabolic cycle is defined by levels of metabolites in the cell increasing and decreasing in regular cycles, which are linked to cell division. Changing feeding conditions for the yeast cells or removing genes from the yeast genome that are responsible for metabolic processes affect the speed of these metabolic cycles.
31 Oct 2023