Annual Report 2017 Biocenter Finland – Annual Report 2015-2016 Biocenter Finland Annual Report 2017 Editor: Antti Siltanen Acknowledgements: We thank the technology platform chairs and BF board members for cooperation in compiling this report. www.biocenter.fi Biocenter Finland – Annual Report 2017 2 CONTENTS FOREWORD ............................................................................................................................................... 4 STATISTICS ............................................................................................................................................... 5 HOST UNIVERSITIES, MEMBER INSTITUTES AND FACULTY .......................................................... 7 GOVERNANCE AND ORGANIZATION .................................................................................................. 9 SCIENTIFIC SUCCESS STORIES............................................................................................................ 11 BIOCENTER FINLAND TECHNOLOGY PLATFORMS ........................................................................ 20 BIOINFORMATICS .............................................................................................................................. 21 BIOLOGICAL IMAGING ..................................................................................................................... 24 GENOME-WIDE METHODS ................................................................................................................ 33 MODEL ORGANISMS .......................................................................................................................... 37 PROTEOMICS AND METABOLOMICS .............................................................................................. 42 STEM CELLS AND BIOMATERIALS ................................................................................................. 49 STRUCTURAL BIOLOGY ................................................................................................................... 53 TRANSLATIONAL TECHNOLOGIES ................................................................................................. 59 VIRAL GENE TRANSFER & CELL THERAPY .................................................................................. 65 NEW PLATFORMS .............................................................................................................................. 68 CONTACT INFORMATION .................................................................................................................... 73 Biocenter Finland – Annual Report 2017 3 FOREWORD The mission of Biocenter Finland is to support where BF is positioned as a major national frontier research in the life sciences by providing infrastructure. The criteria of the interim assessment open access technology platforms and services. BF included the level of development, impact and operates as a nation-wide research infrastructure, significance, as well as openness and collaborative which is distributed to the five Finnish biocenters. use of the research infrastructure. BF was placed in The biocenters and BF are hosted by University of the most advanced category, which is a testimony of Eastern Finland, University of Helsinki, University the success of the BF concept and the quality of the of Oulu, University of Tampere, University of operations. Turku and Åbo Akademi University. BF Since 2017, BF works in close collaboration with establishes, develops and coordinates state-of-the- the Finnish nodes of the Health and Food domain of art technology services and ensures resources for the European infrastructure Projects (ESFRI). The investments into the facilities. The personnel costs Finnish ESFRI nodes are BBMRI (biobanking), are financed by the host universities. More than EATRIS (translational medicine), ELIXIR 2000 research groups in universities, research (bioinformatics), EU-OPENSCREEN (drug institutes and companies in Finland and abroad use screening), EuroBioImaging, Infrafrontier (mouse the BF technology services annually. models) and Instruct-FI (structural biology). The well-established nine technology platforms of Not only ESFRI memberships provide access for BF, Bioinformatics, Biological Imaging, Genome- the Finnish life scientists to research infrastructures wide Methods, Model Organisms, Proteomics and not available at home. Finland is also member of the Metabolomics, Stem Cells and Biomaterials, European Molecular Biology laboratory EMBL and Structural Biology, Translational Technologies and the European Molecular Biology Conference Viral Gene Transfer & Cell Therapy, will be EMBC, but the memberships are not taken fully complemented with three new ones, Genome advantage of. BF is committed to promote to the Editing, Liquid Biopsies and Single-cell Omics. Finnish life scientists’ community the use of the The establishment of the new platforms has begun core facilities and collaboration opportunities that in 2017 with resources that BF obtained from the EMBL offers. EMBC provides funds to the competitive Research Infrastructure Programme of European Molecular Biology Organization EMBO the Academy of Finland (the Finnish Research which offers short and long-term fellowships for Council). young researchers and organizes courses, In 2017, the host universities made new investments workshops, training and conferences. Raising the of about 5 M€, mainly to the Genome-wide awareness of EMBL and EMBC/EMBO started in methods and to the newly established Single-cell 2017 with a BF-workshop for PhD candidates and omics platforms. The universities’ salary support post-docs to showcase what EMBC/EMBO can remained at the 2016 level. offer to support their careers. The choice of the platforms to be established or up- graded is crucial. New platforms must support renewal of science, conform to the needs of established scientists as well as the new generation of researchers, and support implementation of the research strategies of BF’s host universities. Therefore, BF consulted frontier life scientists such as the directors of Centers of Excellence, Academy professors and ERC Starting Grantees on their needs. The choices were consolidated by BF’s Board, where all of its host universities are represented. The year 2017 was marked by an international mid- term evaluation of the Finnish Research Professor Marja Makarow Infrastructure Strategy and Roadmap 2014-2020, Director of Biocenter Finland Biocenter Finland – Annual Report 2017 4 STATISTICS Technology platform funding €40M €30M Figure 1. BF technology platform €20M funding broken down to direct salary support from the host universities, other host university funding, cost recovery from user fees, and other €10M funding sources. The increased other financial support from the host universities was mainly due to increased investments to the Genome-wide methods platform 2017 2016 2015 (4M€), and the new Single-cell Other funding omics platform (1M€). User fees Other financial support from the host universities Direct funding from the host universities to BF platforms Bioinformatics technology platform Electron microscopy Light microscopy Small animal molecular imaging (SPECT/CT) of the RTI unit Genome-wide methods FinnMouse National infrastr. for research on non-mammalian model organisms Protein-proteome platform Metabolomics platform Stem cells and biomaterials Structural biology Protein service for biophysical and structural characterization Biobank technologies Drug discovery and chemical biology Viral gene transfer Single-cell omics Genome editing liquid biopsies Figure 2. Distribution of direct host university funding to BF technology platforms in 2017. Biocenter Finland – Annual Report 2017 5 Users 3000 2250 1500 750 Number of usergroups Figure 3. Number of research groups and non-academic customers 2017 2016 2015 using BF technology platform Local National International Non-academic Total services. Technology platform personnel 160 160 120 120 80 80 equivalents) equivalents) 40 40 Platform personnel (full-time Platform personnel (full-time 2017 2016 2015 2017 2016 2015 Other funding Technicians PhD students Postdoctoral researchers Direct funding from the host universities to BF platforms Senior scientists Figure 4. BF technology platform personnel in Figure 5. BF technology platform personnel by full-time equivalents broken down by source of career stage. funding. Biocenter Finland – Annual Report 2017 6 HOST UNIVERSITIES, MEMBER INSTITUTES AND FACULTY Host universities and member institutes BF is a distributed national research infrastructure Helsinki. HiLIFE includes Institute of that in 2017 consisted of five member institutes Biotechnology and Institute for Molecular Medicine hosted by six universities (Fig. 6). The directors of Finland FIMM as operational units. At University each institute serve as the Governing Board of BF. of Tampere, the Faculty of Medicine and Life Sciences replaced BioMediTech as the member From 2017 on, Helsinki Institute of Life Science institute from the beginning of 2017. HiLIFE is the member institute at the University of Figure 6. The host universities and their BF member institutes in 2017. Faculty At the end of 2017, the Biocenter Finland Faculty J, Jolkkonen J, Jurvelin J, Jänis J, Kaarniranta K, comprised of 413 principal investigators listed Kinnunen T, Koistinaho J, Koistinen A, Korhonen below. Each member institute has used its own R, Kosma VM, Kröger H, Laakso M, Lehto VP, criteria and/or peer review process in