Dedicated Research Facilities

The experimental research laboratories of GBB are modern and well-equipped with all being classified at appropriate VMT levels (ML-I or ML-II) to work with genetically modified organisms (GMOs) and compound thereof, with pathogens, and with mammalian cell lines. All experimental work complies to national (bio)safety regulations in terms of working with GMOs, pathogens, mammalian cell, animals, radioisotopes, and radiation (lasers, X-ray). Through dedicated investments schemes GBB and neighboring research institutes collaborate in acquiring advanced instrumentation and encourage an ‘open door’ policy for making equipment available to researchers in these institutes.

General research facilities and dedicated high-end equipment that is used by GBB researchers comprise amongst others:

• High-resolution Cryo Electron Microscopy: A Thermo Fisher-FEI Talos Arctica with phase plate and direct electron detection camera and FEI-Tecnai 20 transmission microscopes for cryo-EM, immune-EM, and negative staining. Funding for replacement of a lower-resolution TEM (CM12) has been secured via the Sector Plans Chemistry and Biology for installing a new TEM late 2023/early 2024. Access to high-end Titan Krios microscopes has been secured through our partnership in NeCEN (Leiden) and in the Dutch NEMI consortium. For structural analysis, GBB also has access to synchrotron facilities (mostly at ESRF Grenoble, DESY Hamburg, and SLS Switzerland) in case protein crystallography is used to solve structures at the highest resolution;

• Proteomics: Advanced mass spectrometers, nano-flow LC and robotics for proteomics and metabolics; a shared facility operated by Frans Ho and Johan Hekelaar (Strating Institute); additional MS equipment is present in the research groups Molecular Microbiology, Molecular Enzymology, and Molecular Systems Biology, and we have access to the central MS facility managed by FSE pharmacy institute GRIP at the medical campus.

• Cell culturing and analysis: incubators, hoods for culturing mammalian and insect cell lines, extended with a SORP BD FACSAria cell sorter for sorting of microbial and mammalian cells;

• Advanced light microscopy: various confocal, widefield and high-content microscopes are available in the GBB groups Molecular Cell Biology, Cell Biochemistry, Molecular Microbiology, Molecular Systems Biology, Molecular Genetics, Molecular Immunology and Membrane Enzymology. Techniques available at GBB (and the neighboring Zernike Institute) comprise life-time (confocal) imaging, high-content (automated) imaging, correlation spectroscopy (FCS), super-resolution imaging (PALM, STORM, STED) and single molecule studies (single-particle tracking, TIRF, FRET);

• Advanced analytical equipment for (single-)protein (bio)chemistry: SEC-MALS, Surface Plasmon Resonance, ITC, Mass Photometry, Creoptix WAVE System, MST, Nanion Surf system, Optical tweezers extended with fluorescence spectroscopy, electrophysiology, multiple High-speed, Ultra-speed and Analytical Centrifuges, multiple UV/VIS fluorimeters and (stopped-flow) fluorescence spectroscopy;

• Advanced equipment for nucleic acid analysis: Illumina Nextgen and standard sequencers with infrastructure and software to handle, analyze and interpret ‘big data’ from DNA- and RNA-sequencing, (meta)transcriptomics, and metagenomics research;

• Computational resources: Computer clusters to acquire and process large scale microscopy data as well as to perform modeling and molecular dynamics simulations are in house. The computer facilities for quantum mechanics, atomics and coarse-grained simulation, computational protein design, and micromechanics are united in the Berendsen Centre for Multiscale Modelling (directed by Siewert-Jan Marrink). Computational studies are further executed using high-performance computing facilities, either at the CIT department (currently the powerful Hábrók) or externally;

• NMR and GC/LC-MS: Access to NMR facilities (400-700 Mhz) operated at the Stratingh Institute and multiple in-house equipment for small molecule analysis and screening (incl. pipette stations, auto-injectors, and plate readers) using high-resolution LC-MS, UPLC-MS, and GC-MS;

• Cleaning and sterilization of glassware and media is organized centrally at the Linnaeusborg to support 8 experimental GBB research groups, and glassware used for teaching purposes (practical courses);

• Animal facilities: Access to dedicated facilities at UMCG and FSE (Linnaeusborg) for host-microbe studies and the frog terrarium of Julia Kamenz (for non-invasive harvesting their oocytes).