We are highly experienced with the culture of aerobic and anaerobic bacteria and multiple culturing facilities are available in the lab:

• - An anaerobic chamber for culture of strict (intestinal) anaerobes.
• - A culture chamber with low oxygen for microaerophilic bacteria such as Campylobacter jejuni.
• - Culture jars that allow regulation of gas composition.

In the Infection Biology group, we have a strong track record in bacterial infection assays with different host cells. These include immune activation, adherence and invasion assays with immune cells such as macrophages or different types of epithelial cells. Assay read outs include bacterial enumeration, FACS, ELISA, NF-kB activation, qRT-PCR or microscopy (confocal, live or SEM).

CRISPR/Cas technology is revolutionizing the field of molecular biology. We are applying this technique to target genes of interest in mammalian cells to create knockout cell lines. Introduction of targeted mutations or epitope tags is also feasible using our strategy.

Next-generation sequencing of DNA samples of single bacteria or complex microbiota is performed by the Utrecht Sequencing Facility (http://useq.nl).

IgA-SEQ is a technique to identify intestinal pathobionts that are associated with inflammation. IgA-SEQ is performed by Dr. Marcel de Zoete (UMC Utrecht).

Sortagging is a method of protein ligation that allows site-specific attachment of different probes, e.g. fluorescent molecules or biotin handles. The technique is making use of the sortase enzyme of Streptococcus pyogenes that cleaves at a short recognition sequence (LPETG) and can attach a glycine-based nucleophile (GGG-Biotion, GGG-Alexa647). Sortagging can also be performed on the surface of live cells. Labeling of surface receptors with biotin can facilitate immunoprecipitations and reduce background noise to allow identification of interaction partners.

The Center for Cell Imaging (CCI) is a multi-user facility offering advanced microscopic techniques to scientists of the Faculty of Veterinary Medicine and other faculties affiliated with the Utrecht Life Sciences.

Microscopes available at CCI:

• – Leica TCS SPE-II confocal laser scanning-microscope on a DMI4000
• – Olympus BX60 fluorescence mic with color CCD camera (Leica DFC425C)
• – GE Healthcare OMX-V4 blaze Live cell super resolution using SIM
• – NIKON STORM/A1Rsi/TIRF Live cell system with superresolution possibilities
• – Zeiss SLM880 NLO Multiphoton microscope for in vivo imaging
• – Leica S6D preparation microscope

If you are interested in performing mucosal infection experiments in intestine or lung explant tissues of different animals, please contact Maitrayee Chatterjee.