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Annual Report 2014 Swammerdam Institute for Life Sciences Swammerdam Institute for Life Sciences Faculty of Science Annual Report 2014 Swammerdam Institute for Life Sciences University of Amsterdam Faculty of Science Annual Report 2014 Swammerdam Institute for Life Sciences (SILS) Faculty of Science, University of Amsterdam Annual Report 2014 Amsterdam, July 2015 Interviews, text editing and lay-out: Maartje Brink © All rights reserved. No part of this publication may be reproduced, stored in retrieval systems or transmitted in any form or by any means, mechanical, photocopying, recording or otherwise, without written permission of SILS. Table of Contents Table of contents Chapter 1: Management 5 Introduction by the Institute Director 6 Special and Part-time Chairs 8 Management & Contact Details 9 Facts & Figures 10 Chapter 2: Highlights 13 Top publications 2014 14 SILS in Press 16 Grants & Awards 18 SILS Research Day 2014 22 Double portrait of Ronald Koes and Francesca Quattrocchio 23 Interview Frank Jacobs 26 Phd in the spotlight: Jesse Veenvliet 30 Thesis alleryG 32 Chapter 3: Research Programme Cell & Systems Biology 35 Bacterial Cell Biology 36 Synthetic Systems Biology and Nuclear Organisation Group 40 Biosystems Data Analysis 46 Molecular Cytology & van Leeuwenhoek Centre for Advanced Microscopy 52 Chapter 4: Research Programme Neurosciences 61 Structural and Functional Plasticity of the Nervous System 62 Cognitive and Systems Neuroscience 70 Cellular and Systems Neurobiology 78 Molecular Neuroscience 82 Chapter 5: Research Programme Molecular Life Sciences 87 Molecular Plant Pathology 88 Plant Development and (Epi)Genetics 93 Plant Physiology 98 RNA Biology and Applied Bioinformatics 105 Molecular Microbial Physiology 110 Molecular Biology and Microbial Food Safety 116 Mass Spectrometry of Biomacromolecules 122 Annual Report 2014 - 3 Chapter 1: Management Management Midterm Review attitude of this cluster was also mentioned. I am very On 25 November 2013, SILS was reviewed by an happy, satisfied and proud with the outcome of this international committee of scientific experts according evaluation especially because of the high teaching to the Standard Evaluation Protocol 2015-2020 of load that many SILS employees, but especially the the Association of Universities in the Netherlands neuroscientists, experience. This dedication to research (VSNU). The members of the committee were: and teaching cannot be praised enough. Chapeau! professor Stan Gielen, dean of the Faculty of Science of Radboud University, Nijmegen (chair), professor Personnel Judy Armitage of the Department of Biochemistry, The novel research group Plant Development & University of Oxford and Oxford Centre for Integrative (Epi)Genetics including the group of professor Koes Systems Biology; professor Elaine Holmes, head of the of VU University Amsterdam (VUA) and the group Division of Computational and Systems Medicine, of Maike Stam and Paul Fransz of SILS was finally Imperial College London; professor Tibor Harkany, established within SILS. Physically the VU group professor of Developmental Neurobiology, Karolinska moved in the spring of 2015 to their new laboratory Institute, Sweden and Head of Department, Centre and office spaces at Science Park. Dr. Kees Jalink of for Brain Research, Medical University of Vienna, the Netherlands Cancer Institute was appointed a Austria; professor Mike Blatt, professor of Botany, special chair ‘High Resolution Microscopy’ on behalf Institute of Molecular Cell and Systems Biology, of the ‘Genootschap ter Bevordering van de Natuur-, University of Glasgow and editor of Plant Physiology Genees- en Heelkunde’. Also this year, tenure trackers and professor Michiel Kleerebezem, professor in dr Frank Jacobs and dr Jeanette Lorteije were appointed Microbe Interactomics, Wageningen University. in the neurobiology groups of respectively professors I received their final review report on 11 January Marten Smidt and Cyriel Pennartz while eleven PhD 2015. Overall the committee regarded the SILS students, nine postdocs and five technicians/support support facilities (microscopy, genomics, data analysis staff were offered employment by SILS. tools) as excellent while across the board the science practised was evaluated as very good to excellent. The PhD graduations atmosphere within SILS was experienced as open, In total 14 PhD students graduated at SILS this year. friendly and informal while the supportive attitude of Eight PhD students supervised by SILS professors: the staff was praised. Wishwas Abhyankar, Andreas Angermayr (cum laude), The SILS Clusters were also evaluated separately Henrique de Oliveira Cabral, Biju Chellapan, Fleur by the committee. The four research groups of the Gawehns-Bruning, Rosanne Hertzberger, Rachna cluster Cell & Systems Biology are all well-established Pandey and Jesse Veenvliet and six PhD students according to the committee, with the Westerhoff having SILS special chairs as supervisor: Bert van der Introduction the by Institute Director group considered world leading. The committee added Kooij (J. Borst, NKI-AVL), Daan Visser (NKI-AVL, that the bacteriology group has a lot of potential and D. Gadella/K. Jalink), Regina Kanski (E. Hol, NIN), stands out and that the advanced microscopy and data Carlyn Martine-Mamber (E. Hol, NIN), Marie Orre analysis infrastructure is very good to excellent. At the (E. Hol, NIN) and Martine Moeton (E. Hol, NIN). I same time the biology-driven research within this wish them all lots of success in their career. cluster shows some diversity with respect to quality which needs attention. Research grants According to the committee the cluster Neurosciences SILS obtained external research grants with a total performed very good to excellent research, while the value of nearly € 5 million. Most notable was the research of the Pennartz group stands out as world- NWO VIDI grant of € 800.000 awarded to dr Renée wide leading. The translational promise of the group van Amerongen for her research proposal ‘The eternal is high but has yet to be realised. life of stem cells’. Dr Aniko Korosi and Paul Lucassen The cluster Molecular Life Sciences acted as a well- were awarded the NWO Food & Cognition grant of integrated research group that showed a forward € 600.00,-, dr Pernette Verschure obtained an EU look with a clear idea of where to go. The committee Marie Curie ITN grant of over € 600.000, dr Christa also praised the large number of collaborations with Testerink an NWO ECHO grant of € 260.000, dr industrial partners and clearly indicated that the plant Silke Allmann a €250.000 NWO VENI grant and dr scientists of the Cell & Systems Biology cluster fit well Carlos Fitzsimons an ISAO award (100.000,-). within this cluster. The good perspective and positive 6 - Swammerdam Institute for Life Sciences Introduction by the Institute Director Outreach Science in Amsterdam Dr Silke Allmann performed in the TV show Melk In the framework of ‘Science in Amsterdam’ SILS & Honing (Milk & Honey) with the subject ’Do decided to participate in three UvA/VUA interfaculty plants talk to each other?’ while professor Michel collaborations. The Cluster Molecular Life Sciences 1 Haring presented a lecture on ‘Plant Physiology’ at the currently evaluates the added value of a more intense ‘Universiteit van Nederland’ that can be downloaded collaboration with HIMS, the chemistry institute from YouTube. of our Faculty and the Theoretical Chemistry group of VUA. The Cluster Neurosciences explores the Awards collaboration with the VUA Neuroscientists while the The highlight of this year was the granting of the Cluster Cell & Systems Biology is expected to move prestigious Young Heineken Prize to our former PhD to the O2 Building at the VU Campus in the spring student dr. Martin Vinck who is now working as a of 2016 to further strengthen their collaboration with postdoc at Yale University. He obtained this award the VUA Departments Chemistry & Pharmaceutical for his excellent thesis work in the group of professor Sciences and Molecular Cell Biology. However Cyriel Pennartz. because of the ongoing discussions by staff and The SILS ‘Best Research’ Award was granted to the students of SILS and the Faculty of Science about the research groups of professors Hans Westerhoff and added value of an intensified collaboration with VUA Cyriel Pennartz. They were identified as excellent it is not clear if these plans will become reality soon. and world-leading by the SILS Midterm Review Therefore I expect that SILS will continue to exist Committee. This was underlined by the appointment as an interdisciplinary research institute of the UvA of Hans as Fellow of the International Society for Faculty of Science until at least 2018. Systems Biology. The ‘Best Teaching’ Award was obtained by the group of Stanley Brul not because they spent most hours in teaching this year but because this group invested a lot of time and energy in the organisation of teaching activities next to teaching itself. This is also reflected Prof. dr. Willem Stiekema by the positions of Stanley as director of the bachelor Biomedical Sciences, Hans van der Spek as director of the Graduate School Life and Earth Sciences and Gertien Smits as coordinator of the Faculty Honours Programme. The ‘Best Valorisation’ Award was won by dr. Harrold van den Burg for obtaining two grants from the Top Consortium for Knowledge and Innovation Horticulture and Starting Materials that is run by industry, universities and research institutes together and focuses on translational research activities. In total Harrold collected
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