Facilities
The IBB incorporates four core facilities – Biology Imaging Center, Large-Particle Flow Cytometry Facility, the Utrecht Nanobody Facility, and Protein Interactions and Network Analysis – providing cutting edge services to the members of the IBB and external users.
Biology Imaging Center (BIC)
Mission
Biology Imaging Center provides access, support and training in advanced light and fluorescent microscopy techniques for research groups within the department of Biology and also to groups from other institutes within and outside Utrecht. By organizing courses and individual training, the Imaging Center is strongly involved in teaching microscopy techniques to Bachelor and Master students participating in different Life Science programs in Utrecht at different levels. Another important activity of the Imaging Center is development of custom imaging methods and image analysis algorithms and making them accessible to scientific community.
Microscopy techniques
Biology Imaging Center incorporates equipment and expertise on Bright field microscopy, Phase Contrast microscopy, VE-DIC microscopy, regular Wide-Field Epifluorescence microscopy, total internal reflection fluorescence (TIRF) microscopy, laser scanning and spinning disk confocal microscopy. The advanced techniques in which the center currently specializes include multicolor live cell imaging with a high spatial and temporal resolution, 3D live imaging of thick samples using spinning disk and two-photon microscopy, fluorescence recovery after photobleaching (FRAP) and photoactivation, photoablation, laser microdissection and super-resolution localized microscopy (PALM/STORM).
Organization
The head of the Biology Imaging Center is Dr. Ilya Grigoriev.
Large-Particle Flow Cytometry Facility
The selection and purification of molecules, cells, tissues, and organisms of interest are critical yet often time-consuming aspects of biomedical research. Flow cytometers have revolutionized the sorting and analysis of large numbers of individual cells. However, many objects are too large or too sensitive for conventional flow cytometry. For this reason, Union Biometrica has developed large particle flow cytometers able to handle a wider range of object sizes (1 – 1500 µm).
The UU Large-Particle Flow Cytometry Facility provides the life sciences research community in the Netherlands with access to the latest model large particle flow cytometer: the BioSorter. The facility represents the first placement of a BioSorter in The Netherlands, and was established with financial support from the Netherlands Organisation for Scientific Research (Investment Grant NWO Medium), and from Utrecht University (Support Core Facilities, Life Sciences).
Examples of materials that can be analyzed and sorted with the BioSorter are combinatorial chemistry beads and particles, microcolonies of Aspergillus and filamentous bacteria, plant seeds, zebrafish embryos, C. elegans embryos and larvae, Drosophila embryos and imaginal disks, large cells, cell clusters, cultured organoids, and embryoid bodies.
A brand new Sorter Facility is currently under construction. Details will follow soon.
Utrecht Nanobody Facility (UNF)
Mission
The Utrecht Nanobody Facility (UNF) aims to provide support to academic researchers interested in nanobody technology. We provide advice and expertise for development of new nanobodies or new applications with existing nanobodies. In a collaborative set-up we provide the technology for the selection, production, functionalization, and applications of nanobodies. We offer technology for the functionalization of nanobodies using different site-specific conjugation methods of fluorophores (Alexa, Atto, NIR dyes etc.), drugs, nanoparticles etc. Functionalized nanobodies are excellent tracers for imaging purposes and in collaboration with the Biology Imaging Center we provide for single molecule imaging, super-resolution light microscopy, and in vivo molecular imaging.
Technology
Nanobodies are small antibody fragments (15 kDa) derived from camelid heavy chain antibodies. These single domain antibodies are uniquely adaptable tools. Nanobodies can be selected from (custom built) immune libraries, or alternatively synthetic libraries, using phage display. Extensive equipment is available for the thorough characterization of the nanobodies. Important parameters are production yield, stability, specificity, binding affinity, and selectivity in vivo. Nanobodies can be produced at small scale and equipment is available for the large scale production both from E. coli and HEK cells.
Applications
Nanobodies can be used for different applications, such as stabilization of protein conformation for X-ray crystallography and cryo-electron microscopy, protein or vesicle purification, in vitro imaging (both light- and electron- microscopy), as biosensors, and for in vivo imaging. Furthermore, nanobodies can be employed for therapeutic applications, for instance: as antagonists, conjugated to drugs for cancer therapy or fibrosis, as antivirals, for targeted protein degradation, conjugated to nanoparticles carrying drugs, or in immune therapies such as nanobody-based T cell engagers or chimeric antigen receptor T cells.
Protein Interactions and Network Analysis
Mission
Protein Interactions and Network Analysis supports efforts of IBB members to identify protein-protein interactions, and analyze protein interaction networks. We also teach key technologies used to identify protein interactions and methods of network analysis in several courses at the bachelor and master level.
Experimental techniques
We currently support identification of protein interactions at a medium to high throughput scale by yeast two-hybrid. Our services include a complete pipeline including experimental detection, computational analysis of sequencing results, storage in a database, and visualization of interactions though a web-based interface. We have available for screening several C. elegans Y2H libraries, as well as a mouse brain library. Additional libraries can be added on request. For more information on the exact details of the libraries, vectors, strains etc. that are currently available, contact Mike Boxem (m.boxem@uu.nl).
Bioinformatic analysis
In our group we have a long tradition in the bioinformatic analysis and theoretical modeling of protein networks. This means that we can automatically integrate networks obtained from in-house screens with networks from publicly available network data sources such as BioGrid or STRING (which we helped to initiate). Such integrations and further network analysis, such as module delineation, help to pinpoint potential false positives and help to provide biological hypotheses. Integration with complementary data sources such as micro-array data, phosphoproteomic data or evolutionary sequence conservation provide further biological hypotheses for experimental validation. For more information on how to establish a bioinformatic collaboration, contact Berend Snel (b.snel@uu.nl)
Organization
The experimental component of protein interactions and network analysis is headed by Dr. Mike Boxem (m.boxem@uu.nl), and the bioinformatics component is headed by Dr. Berend Snel (b.snel@uu.nl).