V I B

Core Facilities

Technology Suites for Better ScienceScience and technology go hand in hand. New technologies advance science and often accelerate breakthroughs in scientific research. VIB has a visionary approach to science and technology, founded on its ability to identify and foster new innovations in life sciences. The VIB Core Facilities, supported by the ‘Technology Watch’ program, are instrumental in guaranteeing VIB scientists access to the latest and greatest tools and field-specific technologies. The results speak for themselves: groundbreaking research, unprecedented collaborations and real-life applications that change the world.

The Core Facilities are a cornerstone of the research carried out at VIB. As “technology suites for better science”, they offer state-of-the-art servicing in transcriptomics, genomics and proteomics, protein and antibody engineering, advanced light & electron microscopy, and in assay design & proof-of-concept screens. This technoscientific expertise, which would be costly and almost impossible to replicate in individual research groups, is made available to the VIB life sciences research community. Customers have access to cross-platform workflows and novel applications, giving them remarkable competitive advantages.

VIB has 9 institutional Core Facilities in total, providing support in a wide array of research fields and housing specialized scientific equipment and services for each discipline:

BIO IMAGING CORE

PROTEINSERVICE FACILITY

NUCLEOMICS CORE

COMPOUNDSCREENING FACILITY

BIOINFORMATICS TRAINING AND SERVICE CENTER

PROTEOMICS EXPERTISE CENTER

GENOMICSERVICE FACILITY

NUCLEAR MAGNETIC RESONANCE CENTER

NANOBODY SERVICE FACILITY

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Nucleomics Core Facility (NCF) Modern life sciences have become highly dependent on fast access to complex technologies and the ability to interpret huge data sets. The VIB Nucleomics Core Facility (NCF) has developed the expertise to process and analyze challenging samples from a broad spectrum of species, and to subsequently process those samples on next-generation sequencing platforms and other genomics/transcriptomics tools. This means that the unit has the flexibility to run both small and large-scale projects within an agreed timeframe.

In the field of transcriptomics, NCF offers gene expression and miRNA analysis using Nanostring nCounter® technology and small RNA sequencing. For genomic analysis, the facility provides whole genome sequencing and capture-based sequencing (exome sequencing, ChIPseq sequencing and targeted resequencing) using its massive parallel sequencing instrument portfolio. The NCF also uses amplicon-based sequencing workflows for custom sequencing assays, targeted resequencing and metagenomic 16S rRNA profiling.

As an expert unit the NCF offers solutions for mapping and quantifying genomes and transcriptomes that explain phenotypes of interest. With bioinformatics support as an integral part of its service, the solutions truly range from sample to science.

In order to ensure efficiency and swift throughput times, the facility applies the following workflow: consultation and design, sample intake, production, data analysis and delivery. This modular approach also allows the user to pick and choose specific modules.

Nucleomics Core Facility (NCF)

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Genomic Service Facility (GSF)This centralized facility primarily offers high-quality, affordable Sanger sequencing services.

The GSF team originates from VIB’s Department of Molecular Genetics, where it gathered theoretical and practical expertise in high throughput genetic analyses. As well as catering for VIB departments, the team offers classical Sanger sequencing services to third parties and numerous academic and industrial clients. Data processing is performed automatically and in optimal conditions. When required, the GSF also offers consultation and assistance to customers. Years of collaboration with industrial partners have resulted in a setting and a methodology that assure data confidentiality.

In addition to Sanger sequencing, several non-standard services can be provided, such as DNA and RNA extractions and storage, sample quality control and whole genome or gene loci analysis using highly polymorphic markers. Since 2013, the GSF has also been offering access to Illumina technology.

The GSF helps its customers to obtain answers to their genetic questions. As a result, finding variants, mutations and differences in expression, and comparing DNA or RNA between target and control samples, have become accessible for every researcher. With access to the appropriate equipment and high quality in-house expertise, customers are assured affordable assistance and solutions for their research projects. The GSF’s skilled team can also support them in acquiring and comprehending different types of data derived from sequencing or quality assessment.

Genomic Service Facility (GSF)

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Proteomics Expertise Center (PEC)

Proteomics Expertise Center (PEC)VIB’s Proteomics Expertise Center (PEC) provides contemporary mass spectrometry (MS) based proteomics services. This methodology allows for the qualitative and quantitative analysis of proteomes needed to solve a wide variety of protein-related biological questions. Which proteins are in your sample, in which quantity, and what modifications do they carry? How pure is your protein preparation and what are the protein interaction partners of your molecule of interest?

The answers to these questions could lead to the discovery of novel protein biomarkers and drug targets, and assist in the development of novel protein assays.

The PEC provides a diverse set of leading-edge, mass spectrometry-driven proteomics technologies to the whole VIB community, as well as other academic researchers and industrial partners. The services offered include large-scale differential proteome analysis, mapping of protein modifications and interactions, characterization of isolated protein complexes using affinity purification-mass spectrometry (AP-MS), protein quantification using targeted proteomics, protein mass determination, identification of protein partners binding to drugs or small molecules (chemical proteomics) and, finally, comprehensive data analysis and support.

The center has immediate access to several state-of-the-art mass spectrometers to analyze your samples, and offers customized solutions for every project. You will be guided from sample collection to data analysis and the team will assist you in formulating biological conclusions that are easy to interpret for the non-proteomics expert.

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Protein Service Facility (PSF)

Protein Service Facility (PSF) The Protein Service Facility provides service and support in the areas of protein expression, production and purification. It also performs research on new applications. Recombinant production of proteins is one of the most effective procedures used in life sciences research. The ability to produce and purify the appropriate recombinant protein has many applications, including disease diagnosis and treatment. However, the process of producing a recombinant protein is not as simple as it seems and can be influenced by many factors. Therefore, the PSF relies on staff with more than 15 years experience in the field.

Researchers in need of a recombinant protein can turn to PSF to have it expressed, produced and purified. First, a detailed study is conducted on the identity of the protein, considering not just the sequence, but also other physico-chemical characteristics such as folding and post-translational modifications.

PSF customers have access to a large armamentarium of technologies, separately or combined, ranging from FastScreen, FastClean, production, purification and conjugation to protein analytics and research & consultancy.

FastScreen is a 3-4 week feasibility study service for E. coli, Pichia pastoris and insect and mammalian cell expression solutions that are used routinely at the PSF. A protein that has never been produced recombinantly in the past is studied extensively before an expression system is chosen together with various corresponding expression vectors. Finally, FastScreen offers a go/no-go decision for expression strategies to PSF staff. Based on FastScreen data, the project can be continued for production or, alternatively, stopped if the expression results are not satisfactory.

Despite the use of purification tags, classical chromatography is still needed in many steps. If no defined purification method is available, the PSF can offer FastClean, a standardized 2-3 week study to investigate the behavior of samples on a variety of chromatographic media at different loading conditions. The aim of FastClean is to find the optimal conditions to separate the protein of interest from its contaminants.

Depending on the protein of interest, the purification strategy can be based on the physico-chemical characteristics of the protein, the results obtained from the FastClean procedure or on literature.

For several years PSF has also been providing consultancy services to biotech, agro and pharma companies.

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Nanobody Service Facility (NSF)

The monoclonal antibody (mAb), still the mainstay of affinity reagents, can have a number of drawbacks for certain applications. These include the difficulty and expense of pro-duction, bad tissue penetration in vivo and unwanted interactions with Fc-receptors, to name but a few. Furthermore, not every lab is equipped to develop, characterize and/or reformat affinity reagents easily.

Nanobody Service Facility (NSF) makes powerful Nanobody® technology, which lacks the potential problems associated with mAbs, available to both academic and non-academic researchers. The NSF is located at Vrije Universiteit Brussel, where Nanobodies were originally developed. Its services are an excellent way to avoid the inconvenience of get-ting good quality affinity reagents in-house and eliminate the need to invest part of your lab for months in the generation of affinity reagents.

Nanobodies are an extremely useful class of molecules for research, diagnostics and therapeutics in human and animal health. They can be used in any application requiring an affinity reagent.

The NSF has been providing services to academic groups for more than a decade and, more recently, to industrial collaborators as well. In standard service mode, the client provides an antigen to NSF and receives 1 to 10 different Nanobodies for it. The affinity of the Nanobody will be in the range of 0.1 to 100 nM for proteinaceous antigens or from 0.1 to 10 µM for peptidic/haptenic antigens. The whole process, from immunization up to delivery of Nanobodies, takes about four months and has a success rate of about 95%. The NSF team supplies Nanobodies showing a positive score in a relevant assay (ELISA, flow cytometry, etc.) as bacterial clones, along with a full report detailing the results of the immunization, panning, screening and sequence analysis.

Providing a high quality service is important to NSF. Before commencing, the team always enters into detailed discussion with the client in order to define the best modalities for the antigen to be immunized and how it should be handled during panning. The client is informed on how best to express, re-clone and/or purify Nanobodies. The NSF also sup-plies any information the client needs to successfully use the Nanobodies it generates.

As well as generating and identifying Nanobodies, the NSF offers services such as determin-ing affinity, engineering towards higher stability and affinity and humanization of Nanobodies.

Nanobody Service Facility (NSF)

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NMR Expertise Center (NEC)

NMR Expertise Center (NEC)NMR spectroscopy allows visualization of biomolecular structures and dynamics in solution, and complements established structural techniques such as X-ray crystallography and electron microscopy. The Jean Jeener NMR Expertise Center (NEC) provides structural characterization of proteins and protein complexes, which is often an important first step in structure-based drug discovery programs. The services provided by the team can be tailored to help uncover the molecular basis of structure-function relationships, which is eagerly sought in many drug discovery, pharmacological and pre-clinical studies. The center is embedded in the VIB Structural Biology Research Center and provides services to both academia and industry.

Outsourcing your project to the NEC relieves you of the burden of setting up and running your experiment and processing and analyzing the data. This speeds up your research and allows you to concentrate on solving scientific questions. You can rely on highly-skilled personnel to conduct and analyze your experiments and you will receive a final data set for your interpretation.

The services offered range from epitope mapping and establishing structures or binding models of protein complexes, to determining binding affinity for weak protein interactions and describing protein dynamics on multiple timescales. In the near future, NMR-based fragment screening for drug discovery programs will also be part of the portfolio.

In terms of service levels, the center offers you several options. Depending on your needs, we run the experiments on your sample and provide you with the raw data for analysis and interpretation. If you wish, we can also process and analyze the data for you and provide you with the final data set, ready for your use. The NEC team can even train your staff in data processing and analysis.

A little planning is required, as spectrometer availability is essential for fast turnaround times. Once the workload has been defined, scheduling is straightforward and priority scheduling is possible. Experiments run 24 hours a day, 7 days a week, and all data are available immediately.

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BioImaging Core Facility (BIC)The discipline of bioimaging is taking on new dimensions as the ability to acquire, process and visualize structural or functional images of living organisms is becoming paramount for frontline life sciences research. For this reason, VIB has created a multi-site core facility for state-of-the-art microscopy. The facility caters for a wide variety of imaging requirements and covers an array of imaging techniques with high-end equipment. The BIC provides access to experimental design and data analysis, supported by its staff members’ expertise.

The VIB BioImaging Core Facility offers specialist instrumentation for both advanced light and electron microscopy, and develops Correlative Light and Electron Microscopy (CLEM) and super-resolution approaches to answer complex biological questions. The facililty can rely on cutting-edge infrastructure and resources to provide the most suitable instrumentation for any imaging need, thus reducing the learning curve associated with the use of high-end microscopes.

The BioImaging Core Facility has two platform sites in Ghent and Leuven, and serves both academic and industrial life sciences communities. Both sites offer standard services such as confocal and wide-field microscopy, consultancy on experimental design, image acquisition and data analysis. They also give tailored training sessions on image processing and analysis. BIC is your ideal partner for outsourcing some of your imaging and analysis tasks. Its service offering is very flexible and each request will be discussed to define the best approach and tailor it to your needs. Services include hands-on training, access to the appropriate system/equipment, joint projects and more.

The Ghent platform is embedded in the VIB Inflammation Research Center and specializes in high resolution light and electron microscopy to look into cells and tissues in three dimensions. The Leuven platform, which is integrated in the VIB Center for the Biology of Disease, “travels in time” and studies very fast dynamic processes in single cells.

BioImaging Core Facility (BIC)

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Compound Screening Facility (CSF)

Compound Screening Facility (CSF)When screening compound, peptide or siRNA libraries, scientists need robust assays, high-quality screening collections and advanced liquid handling systems. The availability of a range of detection technologies is an additional key to success.

Life sciences researchers can consult the Compound Screening Facility (CSF) on the development of a test system (assay) that reports an underlying biological process. The objective is to develop a ready-to-screen assay that can be used to identify molecules that interfere with the process-of-interest.

Scientists are often confronted with an assay that has a high variability and is too complex for screening. In many cases, they do not have direct access to automation and screening technologies. The facility provides services for assay development, i.e. optimizing and miniaturizing the assay to 96- and 384-well plate formats. The CSF team enhances the technical reproducibility and robustness of an assay and makes it compatible with high-throughput screening. During the entire assay development process, the performance of the assay is evaluated by means of positive and negative controls. Subsequent to assay development, the CSF screens the developed assay using high-throughput technologies and identifies hit compounds through statistical and cheminformatic analysis. After hit identification, the CSF provides services to characterize hit compounds via dose-response measurements on primary, secondary and counter assays, thus allowing the prioritization of hit series. A report containing a list with the selected hit compounds, including the cheminformatic analysis, is always provided and available on request. The raw screening data is also supplied.

Over the years, the CSF has provided support in numerous assay development and screening projects, for both academic and industrial clients.

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BioInformatics Training and Service Facililty (BITS)

BioInformatics Trainingand Service Facililty (BITS) Supremacy of method is the new science paradigm. The use of technology in life sciences research is producing a proliferation of biological data sets. Without bioinformatics know-how, valuable facts remain hidden in the data pile.

Set up in response to the increasing importance of bioinformatics in biotechnology research, VIB’s BioInformatics Training and Service facility provides training and services that contribute to the generation of useful biological knowledge.

The BITS offering is threefold: bioinformatics training, scientific software support and research informatics services.

The facility gives basic and intermediate bioinformatics training to the life sciences research community, focusing on the use of tools and databases to extract useful results from large amounts of raw data. These training courses help researchers to develop indispensable bioinformatics skills needed in modern, data-intensive life sciences.

BITS also provides bioinformatics software for use across VIB’s research areas, with institute-wide licensing available for certain software tools giving free access to VIB scientists. At the same time, BITS addresses the challenge of maintaining bioinformatics software developed by VIB scientists and updating VIB’s flagship bioinformatics software by means of web-based applications, in order to create a larger user base for these tools.

The facility also offers bioimaging informatics services in collaboration with the BioImaging Core facility, and performs extra research informatics services for other core facilities and researchers.

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Remaining at the forefront of technological innovations is of the utmost importance to VIB as a life sciences institute. The core facilities are constantly exploring new avenues to catalyze its scientists’ research and give them a competitive edge. Recently, metabolomics has emerged as an indispensable technology to complement genomics, proteomics, fluxomics and interactome studies. VIB therefore investigated the feasibility of setting up a metabolomics core facility and assessed the investment needed to furnish it with leading-edge technologies and equipment. As a result, a multi-platform metabolomics core facility will be set up in Ghent and Leuven.

Please consult corefacilities.vib.be for more detailed information on the services offered by the VIB Core Facilities and for regular updates on new technologies and applications. The website also provides guidance on workflow procedures and pricing structures.

Contact: corefacilities@vib.b

Conclusion

The Core for Life (C4L) alliance was founded in 2012 with the mission of creating value for the life sciences community by coordinating and bundling core facility expertise and resources across institutes and countries. VIB is one of C4L’s founding institutions, along with CRG, EMBL, MPI-CBG, FGCZ and the Vienna Biocenter Campus-IMP. The alliance capitalises on their reputation as well as its own unique expertise and service excellence to strengthen the position of small and highly heterogenic technology platforms in the scientific landscape, and to provide additional benefits to its members. C4L representatives have defined a set of objectives to help achieve its mission:

• Benchmark and implement good business practices• Share overflow capacity on respective omics platforms• Design a tailored managerial course for Core Facility leaders • Establish cross-facility workflows

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Basic research in life sciences is VIB’s raison d’être. On the one hand, we are pushing the boundaries of what we know about molecular mechanisms and how they rule living organisms such as human beings, animals, plants and microorganisms. On the other, we are creating tangible results for the benefit of society.

Based on a close partnership with four Flemish universities – Ghent University, KU Leuven, University of Antwerp and Vrije Universiteit Brussel – and supported by a solid funding program, VIB unites the expertise of 74 research groups in a single institute.

VIB’s technology transfer activities translate research results into new economic ventures which, in time, lead to new products that can be used in medicine, agriculture and other applications.

VIB also engages actively in the public debate on biotechnology by developing and disseminating a wide range of science-based information about all aspects of biotechnology.

VIBRijvisschestraat 1209052 GhentBelgiumTel. +32 9 244 66 11Fax +32 9 244 66 10info@vib.bewww.vib.be

R.E. Jo Bury, Rijvisschestraat 120, 9052 Gent, België - D/2016/12.267/5