One of the many benefits of being a part of an R1 research institution like UC San Diego is the opportunity to reach out to our bioengineering community for collaborations. If we needed a helping hand or another resource, all we needed to do was cross the street!
Dr. Bradley Moore’s lab has a focus on biosynthesis and marine natural products. In collaboration with the Moore Lab, we were able to observe the metabolic profile of the minimal cell using Gas Chromatography-Mass Spectrometry (GC-MS). The enzymes that make up the pyruvate carboxylase, oxaloacetate acetylhydrolase, acetate-CoA ligase, and pyruvate synthase (POAP) pathway consume and produce a number of central metabolites. An effective way of verifying that the enzyme is successfully functioning within the cell is to identify if these central metabolites are being perturbed in the direction we predict. In order to observe these perturbations, we used GC-MS with the help of the Moore Lab. This analysis strategy also helped us determine any unexpected changes to the minimal cell’s overall metabolic profile. Thanks to the help of the Moore Lab, we were able to ensure that our enzymes were working properly.
Dr. Bernhard Palsson’s lab is focused in the areas of computational biology, data analysis methods, and genome- and cell-scale models. Our team collaborated with the Palsson Lab for sequence alignment and mutation callouts of the evolved thermal resistant minimal cell. The strategy of thermal adaptive laboratory evolution is not to edit a specific section of the genome, but to apply specific, directional pressure to the organism to encourage evolutionary changes. We wanted to understand how the genome of the thermal resistant minimal cell differs from the genome of the ancestral minimal cell. Thank you to the Palsson Lab for their enthusiasm in extending their help to align and call out mutations of our returned sequencing data! We are excited to further work with them to unravel the genes and mutations that are responsible for thermal tolerance.