Kevin Rychel

Abstract The transcriptional regulatory network (TRN) in Yarrowia lipolytica coordinates its cellular processes, including the response to various stimuli. The TRN has been difficult to study due to its complex nature. In industrial-size fermenters, environments are often not homogenous, resulting in Yarrowia experiencing fluctuating conditions during a fermentation.

Abstract It has proved challenging to quantitatively relate the proteome to the transcriptome on a per-gene basis. Recent advances in data analytics have enabled a biologically meaningful modularization of the bacterial transcriptome. We thus investigate whether matched datasets of transcriptomes and proteomes from bacteria under diverse conditions can be modularized in the same way to reveal novel relationships between their compositions.

Abstract Adaptive laboratory evolution (ALE) is able to generate microbial strains which exhibit extreme phenotypes, revealing fundamental biological adaptation mechanisms. Here, we use ALE to evolve Escherichia coli strains that grow at temperatures as high as 45.3°C, a temperature lethal to wild type cells. The strains adopted a hypermutator phenotype and employed multiple systems-level adaptations that made global analysis of the DNA mutations difficult.