Constraint-based modeling of metabolism sits at the heart of many (computationally) systems biology approaches. Classical methods (e.g. flux balance analysis) utilize various optimization principles to predict phenotypic properties from the genotype. While focusing on optimal behavior is a good description for wildtype organisms, characterizing all feasible cellular behaviors consistent with a given set of biological constraints is particularly important for studying non-wildtype behavior.

In this talk, we will introduce (minimal) metabolic pathway analysis to comprehensively and unbiasedly analyze cellular metabolism, discuss challenges in their computation, and highlight applications, especially for rational cell factory design. Finally, we will generalize the concept of minimal functional units to next-generation genome-scale metabolic models. This enables us e.g. to understand the experimentally observed ribosome composition of E. coli (2/3 rRNA + 1/3 protein) as an (evolutionary) resource allocation problem. However, this is only possible if the cellular transcription is constrained too. An observation that strongly questions currently established theories.

Friday, 11 November 2022 @ 12:00 CET

On-site:

University of Vienna
Seminarraum 15
Kolingasse 14-16
1090 Vienna

Online:

https://us06web.zoom.us/j/83157161932?pwd=S1dCMytibUY1cldqR1p3akZBYWlKUT09
Meeting-ID: 831 5716 1932
Passcode: 175842