DC 8: Mode of action studies

PhD project description:

The PhD project will focus on the in vivo characterization of highly specialized genetic elements, bacterial riboswitches. To monitor the biological activity of various riboswitch ligands in cellulo reporter gene assays (employing different bacterial hosts) will be used. Suitable genetic elements must be assembled in plasmid vectors and coupled to a dual luciferase-based test system. The assays will be employed to investigate whether (novel) RNA ligands indeed interfere with gene expression in a dynamic riboswitch system. The experiments will be complemented by SPR studies at UiB.

Further, the antimicrobial activities of the compounds from other working packages will be tested on different target microorganisms (E. faecalis, E. faecium, S. salvarius, S. anginosus, B. faecis, B. vulgatus, A. baumannii, E. coli, C. albicans, off-target: B. obeum, F. prausnitzii, E. limosum) which will be challenged with different levels and combinations of hit compounds and possible antimicrobials. For the most promising ligands, resistant mutants will be studied in greater detail. Whole genome sequence analysis of these resistors will validate the mode of action of the hit compounds (GUF secondment). Sequence analysis employing state-of-the-art data science tools will help us to study possible off-target effects of the hit compounds. If needed to rationalize the data, we will measure compound uptake into target cells using mass spectrometry.

Finally, an indicator E. coli strain for fecal microbiota transplants in vivo will be developed based on the existing reporter gene assays allowing the monitoring of RNA ligands in a microbiome model (secondment GUF).

The candidate is expected to co-supervise MSc-students and participate actively in professional activities within the TargetRNA network, the research group and the Department of Biotechnology.