The IBB incorporates four core facilities – Biology Imaging Center, Large-Particle Flow Cytometry Facility, Nanobody Platform, and Protein Interactions and Network Analysis – providing cutting edge services to the members of the IBB and external users.

 

Biology Imaging Center

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. For more detailed information, see the website.

 

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.

For more details, see http://web.science.uu.nl/developmentalbiology/sorter.html
 

Nanobody platform

Mission

The nanobody platform supports the selection, production and characterization of nanobodies against any possible target. Nanobodies are antibody fragments made from antibodies that lack a light chain, which are found in the camelidae, among which are Llama’s. Despite the absence of a light chain, these heavy-chain-only antibodies have excellent binding properties, fully comparable to conventional antibodies. The Variable domain of the Heavy chain from these Heavy-chain-only antibodies have a molecular size of 15 kDa with full binding capacity. They are indicated as VHH, Nanobody or SDAB (single domain antibody).

Applications of these nanobodies are numerous and people who are interested in this novel technology are encouraged to come up with new idea’s to further develop the possibilities of these antibodies. Examples are: intracellular expression of nanobodies, then indicated as Intrabodies, which may stimulate/inhibit intracellular processes. Intrabodies expressed  as fusion protein with an E3-ligase, induce specific degradation of their target protein. As stabilizing factors of enzymes in their active state for the determination of X-ray structure.  As extracellular ligand for immunofluorescence studies in cells and animals. As targeting divice for anti-cancer drugs, liposomes and micels.

Experimental techniques

Support will be offered for the entire process of nanobody generation, which includes: immunization of Llama’s, library production, phage display selection, screening technology, characterization, production and optimization of the selected VHHs. Selection procedures strongly depends on the demand, and experience is available for different selection strategies such as competition elution, depletion, masked selection etc. Also for further optimization several approaches are available. Nanobodies can be produced in bacteria as well as in mammalian cells. Different functionalization protocols are available such as biotinylation (for IP) and conjugation to different fluorophores (Alexa and Atto dyes as well as dyes in the near infrared (IRDye800CW).

Organization

Paul van Bergen en Henegouwen, email: p.vanbergen@uu.nl
For more detailed information, see our website.

 

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
Y2HWe 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).