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Issue #01 March 2015 Amsterdam Science Hunting for Machines learn Interview starquakes in to interpret Michel Mandjes, magnetars events in video Mr. Network preface index WELCOME TO AMSTERDAM SCIENCE ! Amsterdam Science ABOUT THE COVER IMAGE: Welcome to the very first edition of the magazine . Why this The earliest cell cleavage combination? Amsterdam has a history as a city of scholars. With two universities, stages in an embryo of the sea anemone Nematostella two academic medical centres and more than a dozen research institutes and vectensis. Individual cells are made visible by injecting national research centres, the Dutch capital offers a unique environment for all those RNA that encodes a fluorescent 6 22 fusion protein. More Mr. Networks How mites, moths and captivated by nature and the science developed to describe and understand it. information on pag. 5. butterflies acquired a In an effort to make this science accessible to all we decided to make a bacterial gene to survive on poisonous plants popular science magazine for Amsterdam. Almost a year ago the first steps were taken: organisation of an editorial board, financial support, developing a format with our designers. Although this initiative was born in the Faculty of Science of the University of Amsterdam, the editors ofAmSci soon realised that the many 13 20 Neuregulin-3 tagged as VideoStory: teaching interactions we have with the whole Amsterdam science community called for a impulsivity gene machines to interpret events in wider scope. Scientists from the VU University Amsterdam and CWI were welcomed video footage to the editorial board and the team behind the magazine you are now reading took form. We cover all research areas being pursued in Amsterdam: mathematics, chemistry, astronomy, physics, biological and biomedical sciences, health science, ecology, earth and environmental sciences, forensic science, computer science 11 23 and logic. The core of the magazine is formed by articles from Master’s and PhD Hunting for Starquakes in Eight questions for the dean students, as well as from postdocs and senior researchers. The goal is the same Magnetars – that of communicating the newest and most interesting science taking place in Amsterdam to a broad audience. This is an opportunity to show each other, and the rest of the world, the enormous creativity, quality, diversity and enthusiasm that characterises the Amsterdam science community. Each issue also carries an 14 25 in-depth interview, a column and information for and from alumni. Flame Nebula: a view from “Green gold”: how to use sunlight smartly We are proud of the first edition. It has been quite an adventure, creating a A’ d a m magazine starting from scratch, and we hope you enjoy browsing through some of the best science Amsterdam has to offer. We will have reached our goal if this first issue stimulates you to participate and to submit a contribution via our & more website: www.amsterdamscience.org. If you have any remarks about the content of the magazine or if you have suggestions for interesting subjects, then please 04 highlights colophon contact us ([email protected]). Our special thanks goes to all those 12 then&now who have contributed articles and other material for the inaugural issue, to the Editors in Chief: Hamideh Afsarmanesh; Jeroen Zuiddam 16 column Mark Golden; Michel Haring; Sabine Magazine manager: Heleen Verlinde 17 other members of the editorial board and to our highly organised and irrepressibly Spijker E-mail: [email protected] highlights Members of editorial board: Renée Website: www.amsterdamscience.org 18 cheerful magazine manager, Heleen Verlinde. van Amerongen; Sarah Brands; Harry Design: VanLennep, Amsterdam infographic Buhrman; Eline van Dillen; Swip Draijer; Copy Editor: DBAR 24 alumni Finally, we wish you an inspiring and informative read. Monalisa Goswami; Dorota Kawa; Photographer: Siesja Kamphuis Julienka Mollee; Coralie Pluut; Anne Printer: GTV Drukwerk 26 fun van de Poel; Yash Satsangi; Noushine Shahidzadeh; Héctor Serna Chavez; 27 about On behalf of the Editors-in-Chief, Hans van der Spek; Jocelyne Vreede; 28 André Kuipers Michel Haring 2 3 highlights highlights → Plants grow wherever their seeds → Sunscreens are something that → The sea anemone Nema- → The interior composition of have landed. From that point on, we all use; here comes the sun and tostella vectensis looks deceptively planets orbiting other stars than they do not have the ability to mi- along comes the UV radiation. Ex- simple, but it uses many of the same our own Sun provides a valuable grate to a more friendly environ- posure to UV radiation can cause regulatory genes as more complex constraint for theories of planet ment, so they must be able to adjust sunburn and even skin cancer. Ide- multicellular animals, including formation and evolution. Howev- to their surroundings. This requires ally, the chemicals in a sunscreen humans. This is because humans er, this knowledge is currently very a mechanism that perceives exter- convert this harmful radiation to and sea anemones share a common limited. The recent discovery of two nal conditions, referred to as stress, (harmless) heat on a picosecond ancestor, which lived more than peculiar planets, known by their and then switches on − often multi- timescale. However, prolonged ex- 700 million years ago. By studying catalogue numbers KIC 12557548b PAULA VAN KLEEFF step − signalling pathways leading ERIC TAN posure of the sunscreen still leads ADA DATTOLI our closest living relatives, such as RIK VAN LIESHOUT and KOI-2700b, may change this. to adaptations on the physiological to harmful reactions. Why this oc- Nematostella, scientists hope to un- These planets orbit so close to their PAULA VAN KLEEFF obtained level. ERIC TAN was awarded a PhD curs is still a big mystery – after all, ADA DATTOLI performed her derstand how humans, and other RIK VAN LIESHOUT is PhD stars that the stellar radiation heats her PhD in Biology from the Often this is achieved by mod- from the University of what can happen on a timescale of doctoral research in the complex animals, have evolved and student at the Anton Pannekoek them up to the point of evapora- VU University Amsterdam ification of proteins, for example by Amsterdam on 25 November 2014 picoseconds? section of Molecular Cytology how developmental processes are Institute for Astronomy at the tion. The evaporation peels off their in September 2014. She is attachment of a phosphate group for research conducted at the With this question in mind, we at the Swammerdam Institute organized. University of Amsterdam. outer layers, leading to the ejection currently working as a postdoc Van ‘t Hoff Institute for for Life Sciences of the in the Plant Physiology to specific amino acids; a process Molecular Sciences (HIMS). used high-resolution spectroscopy University of Amsterdam. Our group focuses on early of large amounts of dust, which group at the University of known as phosphorylation. This to demystify the photoprotection embryonic development in Nema- form a tail like that of a comet. Amsterdam. process changes the properties of mechanism of sunscreens by stud- tostella. To study this dynamic bio- These discoveries were made these proteins such as their activi- ying the octyl methoxycinnamate logical process we have developed using the Kepler satellite, a space ty. To maintain a stress signal long (OMC) molecule which is widely a novel live imaging technique: by telescope monitoring thousands of enough, the signalling protein has used as a UV-B filter. This molecule injecting RNA that encodes a fluo- stars for periodic dips in brightness. Guardian to be protected from enzymes that Better is believed to absorb the UV radi- Lighting up rescent fusion protein, we are able The These dips indicate a planet pass- would remove the phosphate group ation and go into a ‘bright’ excited to specifically visualize the actin ing in front of the star, temporar- proteins via dephosphorylation. Eukaryotic sunscreen? state thus using up the energetic animal and tubulin proteins in the cells comet-like ily blocking some of the starlight. cells have proteins, called 14-3-3, radiation before it reaches our skin. that make up the ‘cellular skeleton’ Because planets are almost perfect protect that are able to bind to the phos- Just add Then, in a step where it falls back to development of an animal. These proteins play tails of spheres, the dips caused by planets phate groups on other proteins, the original ground state, it releases an important role in maintaining tend to be symmetric in time. The thus stabilizing and protecting their this UV radiation as heat. Contrary the structural integrity network of dips made by KIC 12557548b and plant’s signalling status. In some ways, the water! to this expectation we found1 out the cell. evaporating KOI-2700b, however, are asymmet- 14-3-3 proteins are guardians of that the OMC molecule makes a This approach has allowed us ric because their dusty tails block stress signalling processes. It is therefore small detour after absorbing the to image different stages of Nema- planets part of the starlight. not surprising that plants carry a UV radiation where it goes into a tostella development, from the By analysing the exact shapes sensors collection of genes that encode for ‘dark state’. The amount of time that earliest cell cleavage events to the of the dips in starlight, we were these guardian proteins. The model it spends in this intermediate state adult polyp. By literally making the able to measure the tail length and plant species Arabidopsis has thir- is actually more than ten thousand skeleton of a subset of cells light investigate how this constrains the teen of such genes. times longer than the desirable up, we can follow individual cells composition of the dust in the tail.