ANNUAL REPORT 2015 Cover Image Embryonic germ cells of Drosophila melanogaster. © Leonardo Gastón Guilgur, IGC. This Annual Report covers the Instituto Gulbenkian de Ciência's financial year from 1st January to 31st December 2015. 2 — Annual Report 2015 3 CONTENTS Visiting Scientists — Barreto, Vasco M. • Epigenetics and Soma 112 4 — External Associated Groups 114 PRIZES & HONOURS 166 2 Prizes & Honours 168 — SUPPORT TO RESEARCH 116 5 Director's Introduction 06 Ferreira, Miguel G. • Telomeres and Genome — Stability 60 Organisation 10 GRADUATE EDUCATION & TRAINING 170 Core Facilities The IGC at a Glance 12 Fesel, Constantin • Lupus and Autoreactive Animal House Facility 118 Budget Overview 17 Immune Repertoires 62 Transgenics Unit 122 PhD Programme in Integrative Biology and A walk through 2015 18 Fonseca, Rosalina • Cellular and Systems Biomedicine (IBB) 172 Neurobiology 64 Plant Facility 124 Gjini, Erida • Mathematical modelling of Bioinformatics and Computational Biology Unit 126 Graduate Programme Science for Development biological processes 66 Gene Expression Unit 128 (PGCD) 176 Genomics Unit 130 Gonçalves-Sá, Joana • Science and Policy 68 Gulbenkian Training Programme in Bioinformatics 1 Gordo, Isabel • Evolutionary Biology 70 Histopathology Unit 132 — (GTPB) 180 Howard, Jonathan • Host-Pathogen Unit of Imaging and Cytometry (UIC) 133 RESEARCH 22 Postdoctoral Training 182 Co-Evolution 72 UIC: Advanced Microscopy Unit 134 In-house Collaborations 24 Janody, Florence • Actin Dynamics 74 UIC: Electron Microscopy Facility 136 Summer Internship 184 UIC: Flow Cytometry Facility 138 Research Groups Jansen, Lars • Epigenetic Mechanisms 76 Theses 186 Adrain, Colin • Membrane Traffic 26 Mallo, Moisés • Patterning and Morphogenesis 78 Service Units Teaching at other PhD Programmes 188 Alves, Filipa • Biophysics and Genetics of Martins, Vera • Lymphocyte Development and Accounting and Internal Audit 140 Morphogenesis 28 Leukemogenesis 80 Administrative Unit 141 Amorim, Maria João • Cell Biology of Viral Mirth, Christen • Development, Evolution and Biosafety Unit 142 Infection 30 the Environment 82 Equipment & Technical Support 143 6 — Athanasiadis, Alekos • Protein-Nucleic Acids Moita, Luís Ferreira • Innate Immunity and General Maintenance 144 Interactions 32 Inflammation 84 Informatics Unit 145 SEMINARS & MEETINGS 190 Baena González, Elena • Plant Stress Oliveira, Raquel • Chromosome Dynamics 86 Library 146 Signalling 34 Oliveira, Rui • Integrative Behavioural Biology 88 Research Funding Affairs 147 Seminars at the IGC 192 Becker, Jörg • Plant Genomics 36 Parkhouse, Michael • Infection and Immunity 92 150 Meetings at the IGC 204 Beldade, Patrícia • Variation: Development and Penha Gonçalves, Carlos • Disease Genetics 94 Research Structures & Networks Selection 38 Pereira Leal, José • Computational Genomics 96 Presentations by IGC Researchers Bettencourt Dias, Mónica • Cell Cycle Perfeito, Lília • Evolution and Genome - at international meetings and seminars 208 Regulation 40 Structure 98 - at national meetings and seminars 215 Carneiro, Jorge • Quantitative Organism Rocha, Luís M. • Complex Adaptive Systems 3 Biology 42 and Computational Biology 100 — Castro, Diogo S. • Molecular Neurobiology 44 Soares, Miguel • Inflammation 102 PUBLICATIONS 152 Chaouiya, Claudine • Network Modelling 46 Sucena, Élio • Evolution and Development 104 7 — Chelo, Ivo • Eco-evolutionary Genetics 48 Teixeira, Luís • Host-Microorganism Peer-reviewed publications PUBLIC ENGAGEMENT IN SCIENCE 218 Chikhi, Lounès • Population and Conservation Interactions 106 In-house publications 154 Genetics 50 Telley, Ivo • Physical Principles of Nuclear Epub ahead of print 161 Demengeot, Jocelyne • Lymphocyte Physiology 54 Division 108 IGC current address 161 Science Communication & Outreach 220 Domingos, Ana • Obesity 56 Xavier, Karina • Bacterial Signalling 110 Book chapters 162 Fundraising 225 Duque, Paula • Plant Molecular Biology 58 Associated groups publications 164 Acknowledgements 227 4 — Annual Report 2015 5 THE DIRECTOR’S INTRODUCTION — Jonathan Howard "A sacred grove of olive trees ence itself, both conceptual and technical, but also election, and the coming into power of a new socialist against funding constraints, career difficulties and government. In the recent political history of science dedicated to Athena, the goddess intense competition. Their successes are hard-won in Portugal three socialist governments in the period of wisdom, outside the city walls and the failures bitter. Our scientists today oscillate from mid 1995 to June 2011 were characterised by a of ancient Athens" between triumph and disaster, with the triumphs powerful endorsement of science and its integration made that much more glorious, and the disasters that into large-scale national programmes of infrastruc- much more emphatic by amplification from the pub- ture development in higher education, science and licity delivered by the outside world. technology. For now, for the IGC, the arrival of a new Out of the city, alone in its beautiful garden, dedicat- socialist government in November 2015 stimulates ed to wisdom, the Instituto Gulbenkian de Ciência The outside world has very much to do with the IGC new speculation about future science policy. The rap- seems to be the very epitome of the Academy, an un- because, Academy or not, the IGC relies entirely on id strengthening of Portuguese science during the troubled space where "this intellectual being, these its ability to persuade the outside world to pay for it. last socialist governments coincided with a vision- thoughts that travel through eternity" can live and The Calouste Gulbenkian Foundation, our owner and ary Minister of Science, Technology and Higher Ed- grow in peace. We are separate from the hurly-burly the owner of our legal identity, needs to know and ucation, Mariano Gago and a GDP that grew about of the city, yet its pleasures, beauties and excitements understand what it is that we do, why we do it and 39% from 2000 to 2008, while the collapse of Portu- are close at hand. On a smaller scale it somehow re- how well we do it. Both our individual projects and gal's economy after 2008 was inherited by the social calls the relationship between the "dreaming spires" the IGC as a whole are subjected to constant evalu- democratic government that took power in 2011 and of Oxford or Cambridge and the great metropolis, ation by the outside world, whether it is our interna- despite the best intentions, led to a reduction in the London, or perhaps between Princeton and New York tional Scientific Advisory Board that reports to the funds available for science. Now we have a socialist City, or Caltech and Los Angeles. This almost anti- Foundation on the whole IGC every year, the review government, again publicly dedicated to strengthen- thetical relationship between the academy and the committees of the ERC and other national and inter- ing the national science programme, but this time city has been around for a long time. It is not an op- national grant agencies who review our research pro- with the economy in dire straits. What can we hope position, the contemplative life and the civic life both jects and programmes, and the editors and referees for, what can we expect? More resources for competi- belong to the make-up of mankind, but rather a com- of the journals in which our research is published. tive research funding would be marvellous, but with plementation. Most recently the IGC was evaluated in its entirety a static national budget and many demands on it, this in the course of the programme to institute the new may be hoped for but certainly not expected. In the Is this indeed the IGC, or only what it seems to be? Unidades de Investigação e Desenvolvimento (Units absence of this, what not only the IGC, but surely all Scientific research in the 21st century is very, very of Research and Development). This evaluation was research organisations in Portugal must be begging different from the monastic disciplines that gener- conducted on behalf of the Portuguese national re- for is coherence, planning and to the extent possible, ated the modern academy. I remember, it must be search funding body, the FCT, during 2014 by a stability at the level of the national research fund- more than 40 years ago, as a PhD student working reputable international organisation, the European ing organisation, the FCT. There is no "right" level on lymphocyte recirculation, wandering through the Science Foundation, using exclusively referees from of funding for science because there are too many beautiful cloisters of the University of Pavia, admir- outside the Portuguese scientific community. The controversial issues to reconcile. It is only inevitable ing the memorials to Gaspard Aselius "quis primus IGC was honoured with the highest commendation of that small, poor countries will invest smaller sums incognitas vias chyli deprehendit"1 and Camillo Gol- "Exceptional". It is particularly sad for the IGC that than large rich ones and less science will be done. gi. But behind the walls of the cloister, seen through the meaning and value of this eminent rating was But it is not at all inevitable that the funds available, the elegant windows, the rooms of the (at that time) obscured, overshadowed and possibly even called in however meagre, should be distributed so erratically renowned genetics department were filled with giant question by the politically-charged furore that broke that research planning is virtually impossible. If the computers, symbols