University of Basel is the oldest Swiss university with a full range of subjects covered in teaching and research. The Department Biozentrum combines 30 independent groups that cover a wide range of molecular biology subjects such as Infection Biology, Neurobiology, Growth and Development, Biophysics and Structural Biology, and Computational and Systems Biology.
The Bumann lab focuses on Systems Biology of Infection and coordinates the RTD project “BattleX” involving 6 widely recognized partners that together investigate host/pathogen interactions (funded by the Swiss Initiative for Systems Biology SystemsX with CHF 5.0 Mio).
Role: Within this collaboration the experimental group (i) purifies Salmonella from infected mouse tissues using flow cytometry (FACS), (ii) determines absolute in vivo copy numbers for porins and efflux pumps using shot-gun and targeted proteomics approaches (mass spectrometry-based), and (iii) generates mutants with altered porin and efflux pump expression. The computational team combines these data with kinetic parameters for porins and efflux pumps as determined by the other partners to obtain a quantitative and predictive computational model for envelope permeability.
Key facilities and infrastructure: UBS has state-of-the art equipment and extensive expertise for pathogen purification from infected rodent tissues (using FACSsorting), and proteome analysis of the purified samples using shot-gun mass spectrometry. This includes a four-laser sorter equipped for BSL2 aerosol management to ensure safety of operating personnel; several Orbitrap-Velos mass spectrometers with very high mass accuracy and excellent sensitivity; sophisticated software packages for protein identification and absolute quantification. The equipment is operated by especially trained specialist personnel. In addition, fully equipped microbiology labs are available for cultivation under various conditions including various levels of hypoxia.