50Th Anniversary EMBO Members Meeting 2014

WINTER 2014 | 2015

ISSUE 29

50th Anniversary The EMBO Meeting is EMBO Members coming to Birmingham Meeting 2014 page 4 pages 10 – 11

Meet the scientist Michael Potente pages 6 – 7 EMBO Young Investigator Investigator EMBO Young

News Bringing data to the fore: Interview We need a CERN for Feature Euro-BioImaging: Open access The SourceData project enters genomics: Emmanouil Dermitzakis infrastructure for imaging technologies. proof-of-principle phase talks to Thomas Lemberger.

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appointed members of the Scientific Advisory Bringing data to the fore Board will provide us with essential guidance in this respect.” The SourceData project improves access to the data in published scientific The Scientific Advisory Board ofSourceData articles and enables further use of research results. This EMBO initiative includes Jason Swedlow, of the University of has entered its proof-of-principle phase with the support of the Robert Dundee, Scotland, Alfonso Valencia, Director of the Spanish National Bioinformatics Institute, Bosch Foundation. The tools that are being developed as part of the project Susanna-Assunta Sansone, of the University make the source data in scientific publications easier to find and allow of Oxford e-Research Centre, Phil Archer, Data scientists to use the data to their full potential. Activity Lead of the World Wide Web Consortium, and Mark Patterson, Executive Director of eLife.

fficient access to primary research could essential findings in the paper to the reader. At The SourceData website will be launched in significantly speed up science. Yet scientific EMBO Press, dedicated scientific data editors April at sourcedata.embo.org Ejournals publish most data as figures that already work with the authors of manuscripts to do not easily allow further analysis of the data optimise and structure the presentation of their and are inaccessible to systematic data mining or figures and data. search. “When I had to make an extensive review SourceData recently hired its first biocura- of all papers reporting Cdk1 substrates, I realized tors who joined EMBO in Heidelberg, Germany. how cumbersome and time-consuming such an “Part of our job is to annotate the figures of elementary task can be using standard literature papers published in open access and other part- search engines like PubMed, let alone finding and ner journals. We collaborate with publishers, comparing the respective figures showing the including EMBO Press, Wiley, HighWire Press experimental evidence,” Tim Hunt explains to and Nature Publishing Group, to make a proof- Figure source data illustrate this problem. “It would be so wonderful of-principle demonstration of the capabilities to be able to find and compare all published cell of the SourceData curation process and seman- The source data underlying figures are published alongside the illustrations cycle-dependent phosphorylation profiles of such tic models that we are developing,” says Sara under the terms of a CC0 licence to substrates to analyse the differences, depending El-Gebali, one of the new staff. “We are working promote unrestricted re-use. on the context of the experiments.” To address closely with the software developers at Vital-IT to this central issue in scientific publishing, EMBO optimize the usability of the curation tool.” has initiated the SourceData project. SourceData “Our goal is to transform the scientific paper will develop tools adapted to the scientific into an enriched resource,” says Thomas publishing process that will make published data Lemberger. “We want to make scientific papers re-usable and searchable. more useful to the community and the data in “The main objective of the SourceData project them more easily discoverable. One of the ways is to describe the biological content of the data to do this is to publish the data in a more struc- underlying published figures—we call these tured manner and in a form that is accessible to ‘source data’—by using standardized terminolo- computers. The first paper published by EMBO gies and developing data-oriented strategies to that included source data was published in search the literature,” explains Thomas Lemberger, Molecular Systems Biology in 2009. More jour- Descriptive metadata Deputy Head of Scientific Publications at EMBO, nals are adopting similar policies. We can now Essential semantics of published who leads the project. build on this experience to go full circle: Soon experiments are represented in a “All EMBO Press journals already encourage we will be able to publish figures in a way that machine-readable way using the presentation of source data for figures that not only includes the human-readable illustra- standardised terminologies. convey the essential findings in a paper,” says tion and figure legends but also the associated Bernd Pulverer, Head of Scientific Publications at source data and machine-readable metadata. EMBO. “Last year, more than half of the research This is a very exciting time.” SourceData collabo- papers in our journals contained source data and rates with publishers including Wiley Blackwell we are confident that this will become the stand- and HighWire to ensure the tools are applicable ard for publication in the near future.” across journals. The SourceData project has recently received “It is an essential part of our job to work in support from the Robert Bosch Foundation to collaboration with our publishing partners Wiley develop the necessary software tools in collabo- and HighWire to optimize the integration of bioc- ration with the Vital-IT Center for high-perfor- uration tasks within the production workflows. mance computing and the Swiss-Prot groups, We also need to develop downstream applica- Data-oriented search both headed by Ioannis Xenarios at the Swiss tions such as ‘Smart Figures’ that will allow read- The web of connected data can be Institute of Bioinformatics. One of the tools is ers to view figures in one paper in the context searched to help researchers find the a computer-assisted biocuration platform that of related data published in other papers,” says data they need and the papers where helps biocurators to identify in an unambigu- Nancy George, biocurator at SourceData. “We they were published. ous way the biological components involved in also need to keep up to date with innovations a published experiment. In addition, whenever in the fields related to biocuration as well as the possible, a simplified computer-readable repre- development of community standards and data sentation of the hypothesis tested by the experi- exchange formats.” Further reading: Lemberger T (2010). From bench to website. Molecular ment will be generated. “For a project like SourceData, we need to Systems Biology 6: 410. With the biocuration tool in place, editors of combine expertise in areas like scientific publish- Lemberger T (2014) Tools of discovery. Molecular Systems scientific manuscripts can describe the source ing, data mining, semantic web technologies Biology 10: 715. data underlying the figures that represent the and biocuration,” says Lemberger. “Our recently

them at the top level in the civil service: Grade 1 permanent secretary level so they would have In the public limelight real clout in the hierarchical civil service and give them an appropriate staff, about 130 people to do Lord Robert May has had a distinguished the things they wanted to do. When they lost the election, a Tory peer, William Waldegrave, who career that has spanned continents and was a very good friend of science, convinced the research disciplines. From 1995 – 2000, he winner, John Major as Prime Minister, to imple- served as Chief Scientific Advisor to the ment the Labour Party manifesto.

United Kingdom Government followed by And you were thrown immediately into several five years as President of the Royal Society. crises? He talked to Barry Whyte about his career I enjoyed it very much. There were some quite interesting excitements on my watches. There and achievements at the 50th Anniversary have been on later ones. One of them motivated EMBO Members’ Meeting held in October me to do what I think was the most important last year. thing I did in the five years that the appointment was for – which was to actually issue protocols for science advice in policy making. One has to understand that the Chief Scientific Advisor’s job I read that throughout your career you have than that but it is largely driven by the fact that is essentially to tell you what the facts are that liked to get in early to tackle problems. You there are more people and that is part of a much constrain the political process of deciding what to prefer to get in quickly to a new area as opposed larger question. do. But ultimately the Science Advisor can’t tell to looking at more established ideas? you simply what you should do. They can only In some ways, when people ask me about my How did you make the leap into public affairs? set out what are the facts, which point maybe career, I have to say I have a short attention span Well [my wife and I] had been at Princeton to a particular action. You are painting the back- –that is why I keep hopping around. The truth is University for about 16 years or so. I had been drop for, as it were, a drama in which the play that I like the early stages of problems, when the one of the senior administrators. Princeton had will then be acted out as a democratic process in area is not too crowded and there are interest- a President and a Vice President and then four parliament. ing problems that have never attracted as much major Deans, one for the faculty, one for the undergraduates, one for graduate students and Isn’t it true that science works on the basis of one for research. The [post] for research was a skepticism and questioning and that this is “The truth is that I like the early legacy of World War II when they appreciated sometimes very difficult to convey to a wide stages of problems...” there was going to be much more government audience? support for research at universities. Princeton Absolutely. Sometimes people want to hear the is most unusual in having rules that say yes we answer that they would like to hear and it is not attention as I think they should have. When I do want people to be doing good research but we welcoming that they are to be told that it is not get into something new it has been my habit not want it to be basic research. It may not actually the right answer. It is not the job of the Chief to read too much about it – just to read a little bit involve developing a product that is very much Scientist to say its not the right answer, here is and get a grasp of what is the problem. Then I against the temper of some of the times today. the right answer, this is what you must do. Point think about how I would go about understanding That’s the sort of place it was and I think it prob- out that you think it may not be the best but you it better. I try to learn about “the what” ques- ably still is. have got to respect the democratic process. tions but I do not spend much effort on what are the “tentative why” questions, which are by and You were approached to be Chief Scientific In 2014, EMBO enlarged its communities large lacking. I think if you read too much about Advisor of the United Kingdom? of ecology, neuroscience and evolution. what the current state of progress is on both “the The history of this particular job is an interest- What future directions might this take the what” and “the why” it will tend to channel your ing one. Let me begin with that. There was in organization? thinking. the labour party in Britain in the 1990s a very I wouldn’t be so bold as to venture looking into interesting figure behind the scenes called Jeremy the far future. It seems to me certainly a good There is a statistic out there that 80 – 90% of Bray. He was a very original thinker and not inter- idea. Molecular biology is doing great things but all scientists who have ever been alive are alive ested in political advancement. He convinced from my perspective it does tend to be a little today. We live in a very different environment Neil Kinnock about the importance of this post. focused on accumulating experimental evidence, and there is a lot of pressure on younger The position of Chief Scientific Advisor had been which is hugely important. I have always thought scientists. Is it really more difficult today to be hugely important in World War II and in the that when it finally begins to mature it is going a scientist? subsequent years it went down and down. In the to go a bit wider and it is going to ask larger I think so. I would be surprised if it wasn’t. My 1970s, it was half a day a week when the person questions beyond what is there. You want to go reply is purely a conjectural one because I am not who held the job met not with the Prime Minister somehow right back to seeing how did it get to as familiar with the facts of younger careers as I but with his top policy group. Mrs Thatcher be like that and why did it get to be like that. So might be but it many ways it is just one aspect began to bring it back up again. She created the I think it can only be for the good of everybody of a much wider problem. It is not just that there advisory committee on science and technology. that the knowledge base and the enquiry base – are more people wanting jobs in science but part- She had a very good person as her advisor but in the interests simply of pure molecular biology – ly, not entirely, it is that there are more people. Jeremy Bray went beyond this. He suggested in broaden out to ask questions about evolution and There are more young people than there ever the early 1980s to Neil Kinnock, who was expect- ask questions about the ecological environment have been and so it would be interesting whether ed to win the next election for the Labour Party, in which simple things happen. the increase in numbers of people wanting to go that one of the manifesto commitments would into science is simply proportional to the extra be to create a formal office of science and tech- increase in young people. I think it is a bit more nology. Bring in someone from outside, appoint

The EMBO Meeting advancing the life sciences comes to Birmingham 2015 The 6th EMBO Meeting will take place at the ICC in Birmingham, Birmingham United Kingdom England, on 5–8 September 2015. “The EMBO Meeting is a fantastic opportunity to learn about the latest developments in the life 5 – 8 September sciences across a broad range of topics,” says EMBO Member Gillian Griffiths, Professor at the Cambridge Institute for Medical Research and one of the organizers and chairs of this year’s meeting. “I’m very excited that the meeting will be held in the United Kingdom.” The event takes place at the ICC, one of Europe’s high-profile conference venues that typically hosts over 350 meetings and more than 300,000 delegates annually. A central location in the United Kingdom makes it a perfect choice for The 6th EMBO Meeting

he EMBO Meeting encourages scientists to “The EMBO Meeting is all about the commu- look beyond their own fields, engage with nity of life scientists in Europe and beyond’” says Tthe international scientific community and EMBO Director Maria Leptin. “It allows scien- explore interdisciplinary approaches to research tists from all countries in Europe to hear talks in the life sciences. Participants experience new by leading international researchers from all over perspectives on topics that cover the entire range the world. Young scientists also have access to of the life sciences – from studies of molecules career opportunities through networking events and the cell all the way up to investigation of larg- and other career-related activities.” The meeting er, complex biological systems. More than 1000 will also include a full range of options for exhibi- scientists are expected to attend. tors to interact with attendees as well as poster This year’s meeting includes 20 concurrent sessions where researchers can present their sessions that take a comprehensive look at biol- work to the wider scientific community. give keynote lectures covering non-coding ogy from the perspective of molecules, cells, The plenary lectures will look at nuclear RNA-protein complexes and the unfolded protein the organism and the very latest methods that architecture, pathogens and defense and stem response, respectively. Other confirmed speakers researchers use to study the life sciences. The cell biology. Joan Steitz from Yale University at the meeting include Stephen P. Jackson, Robert sessions include talks from more than 50 scien- School of Medicine and Peter Walter from the Martienssen, Daniel St Johnston, Azim M. Surani, tists from around the world. University of California, San Francisco will and Inder M. Verma. EMBO Young Investigator Claudine Kraft, a Group Leader at the Max F. Perutz Laboratories at the University of Vienna, Austria, remarks: “Our work focuses on the signalling events and molecular steps leading to the induction of autophagy, the waste disposal system of a cell. Defects in autophagy are involved in numerous diseases, including cancer and neurodegenerative disorders such as Alzheimer’s and Parkinson’s disease, yet little is known about the cellular mechanisms that lead to these conditions. I am very much looking forward to presenting our latest findings at the meeting in Birmingham.” EMBO Member Philippe Sansonetti, Professor at the Pasteur Institute and the Collège de France in Paris adds: “My talk will address how the concepts and tools the-embo-meeting.org of the cellular microbiology of bacterial pathogens can be adapted to study the symbiotic interaction between the gut microbiota and the host intestine.”

EMBO Advanced Fellowships The newly elected EMBO Advanced Fellows are: Five researchers to receive two years of additional funding ➔➔ Suewei Lin, University of Oxford he quality of the applications was very Four of the successful candidates are based in ➔➔ Julia Santiago Cuellar, “ high, five candidates were outstanding,” the United Kingdom, one in Switzerland. “Being University of Geneva Treports Andrea Hutterer, Manager of the awarded the EMBO Advanced Fellowship allows ➔➔ Grzegorz Sarek, Cancer Research UK EMBO Fellowships Programme. Five successful me to finish my current postdoctoral project and London Research Institute candidates were announced in 2015 to receive the take the first steps towards becoming an inde- ➔➔ David Schwefel, MRC National Institute new Advanced Fellowship, a scheme introduced pendent scientist,” says one of the awardees, for Medical Research (NIMR) last July. This new funding allows former and Julia Santiago Cuellar, currently working at the ➔➔ current EMBO Fellows to apply for an additional University of Geneva. “The award is a sign of trust Emily Wong, EMBL-EBI, Hinxton two years of financial support. and recognition to European researchers will- By introducing this scheme, EMBO followed ing to pursue their scientific careers.” Grzegorz up on suggestions from the community of EMBO Sarek from Cancer Research UK London Research Application deadline Fellows to extend the timeframe of the funding Institute comments: “ This fellowship gives me for senior postdoctoral researchers. Many of the a fantastic opportunity to take my research to The 2015 deadline for submission is 1 July. postdoctoral scientists struggle to complete their another level. EMBO Fellowships are one of the scientific projects within the two years when they finest programmes for postdoctoral scientists More information: receive the stipend. Last year it was decided to seeking to advance their career.” www.embo.org/funding-awards/ grant an extra period of funding to those showing fellowships/advanced-fellowships exceptional progress and potential to establish quickly their independent line of research.

presented evidence that both cell-intrinsic and systems such as cancer. Lukasz Swiech, from the EMBO Fellows cell-extrinsic factors can lead to de-differentiation Broad Institute spoke about the use of adeno- of cancer cells to a stem cell-like state. His talk associated virus (AAV)-mediated Cas9 delivery reiterated the incredible plasticity of cancer cells into the brains of living mice, enabling the target- meet at the Salk and the obstacles the field still needs to overcome ing of single or multiple genes into specific neural to prevent tumour relapse. cell types. Institute Oren Ram from the Broad Institute presented Besides fascinating talks on research discov- an interesting talk describing his profiling of eries, I also enjoyed the talks from junior prin- 120 past and present EMBO Fellows a large number of chromatin regulators at the cipal investigators Andrew Holland from Johns working in the United States came single cell level by combining ChIP-Seq with Hopkins University and Cristina Lo Celso from microfluidic technology. His talk highlighted the Imperial College London who described their to the biennial meeting held in San importance of using single-cell profiling to tease career paths as EMBO Fellows. At dinner, Cristina Diego in November 2014. Elisabete out molecular mechanisms in heterogeneous gave me and other EMBO Fellows great advice Nascimento, postdoctoral on the do’s and don’ts of starting your own laboratory. Valuable infor- researcher at Stanford University, mation on funding options available reports on the three-day event. EMBO US for junior researchers who wish to Fellows’ return to Europe and start their s a second-year postdoctoral fellow at laboratories came from Isabelle 2014 Stanford University, it is easy to get – November Vernos, member of the ERC Scientific Aengrossed in the daily experimental work Council and Guntram Bauer from the and forget that interactions with fellow scientists Human Frontier Science Program. are just as important for a successful scientific Finally, Dena Plemmons, University career. Attending the sixth US EMBO Fellows’ of California, San Diego, initiated an Meeting at the Salk Institute came as a breath interesting discussion on research of fresh air. During the three days in sunny San integrity, using several examples of Diego, I experienced a friendly atmosphere and ethical issues that happened in real life. many chances to network with the more than one I found the meeting very produc- hundred EMBO Fellows living and working in the tive, providing me with advice and United States and Canada. information crucial to my career as The meeting started off with a fascinating a young scientist, and allowing me welcome talk on plasticity versus hierarchy in to network with highly skilled EMBO cancer stem cells by EMBO Member Inder Verma, Fellows. I would recommend all who hosted the event. As a leader in develop- EMBO Fellows in the United States ing virus-based gene therapy vectors, he has and Canada to attend these meet- used engineered viruses to express oncogenes in ings as they help you build your own glial cells and neurons, demonstrating that the scientific career. introduction of oncogenes in this way leads to Elisabete Nascimento, development of glioblastoma regardless of the Stanford University cell of origin. He also discussed cell plasticity and

©2015 EMBO EMBOencounters | Winter 2014 | 2015 | [email protected] 5 news from the embo community Meet the scientist EMBO Young Investigators & Installation Grantees 2014 EMBO Y 2014 EMBO Y oung oung I nves I nves t iga t iga t t or or ax F. Perutz Laboratories Perutz ax F. we Dettmar © U © M Michael Potente Claudine Kraft Max Planck Institute for Heart and Lung Research, Bad Nauheim, Germany Max F. Perutz Laboratories, University of Vienna, Austria

Research focus. Our research focuses on blood vessels, particularly the regu- Key career experience. At high school I was fascinated by physics, math- lation of blood vessel growth (angiogenesis) by metabolism. Angiogenesis ematics, chemistry, and also by genetics, although we merely touched and metabolism are intimately connected, as blood vessels provide nutri- upon it. Not quite sure which of these interesting paths to follow, I was ents and oxygen to energy-consuming tissues. We study how blood vessels advised to consider biochemistry. One day I walked into the laboratory of sense their metabolic microenvironment and how they use this information Gottfried Schatz at the Biozentrum Basel to inquire about an internship. I to build vessel networks of organ-specific size, shape and function. We are had only just finished school, but he accepted me for a three-month train- also interested in the metabolism of endothelial cells (the cells that line the ing. It turned out to be an invaluable experience and the basis of my future inner surface of blood vessels), aiming to understand how changes in meta- career as a biochemist. I still turn to Jeff’s advice when confronted with the bolic state impact vascular growth and homeostasis. ups and downs of life as a scientist. For my postdoctoral research, I joined the group of Matthias Peter at the ETH in Zurich. Since I was interested in Medical background. I was trained as a clinical cardiologist, but I always protein degradation and wanted to work with yeast, his group turned out to had a strong interest in basic science. Already as a young medical student be an ideal choice. Matthias already had plans to work on autophagy and I was fascinated by biochemistry, molecular signal transduction and the he let me establish my own line of research. mechanisms of disease. I cannot say it was a concrete decision to focus on basic science. It was rather a continuous development. Encounters with EMBO. My relationship with EMBO is deeply rooted: As a PhD student I worked in the laboratory of former EMBO Young Investigator How different is basic science from medicine? I think medicine has tradi- Jan-Michael Peters and as a postdoctoral researcher I was granted an EMBO tionally been more hierarchical, but this is beginning to change. I was lucky Long-Term Fellowship. Jan-Michael was a great role model and mentor for enough to do my medical training in a very science-oriented department in me. He gave me a chance to join the Young Investigator PhD course offered Frankfurt, where a lot of emphasis was put on cooperation. This collabora- by EMBO. Now, more than ten years later, I can send my own PhD students tive environment helped me build up my research programme in the early to this course. I am very proud of being selected as a Young Investigator days of my career. myself.

Changing directions. My research interests have not changed much Recent research. We are interested in the function and regulation of the throughout my career. I guess this is, in part, a consequence of our scientific cellular waste disposal system called autophagy. Defects in autophagy are approach. Our research is primarily driven by observations of our model involved in numerous diseases, including cancer and neurodegenerative systems rather than hypotheses. We try to look very carefully at phenotypes disorders such as Alzheimer’s and Parkinson’s disease, yet little is known and then formulate questions that will help us understand the underlying about the cellular mechanisms that lead to these conditions. A special focus mechanisms. of my team is the function and regulation of the Atg1 kinase complex, a major regulator of autophagy in yeast as well as in humans. Its function Selection as EMBO Young Investigator. To me, it is the package that makes still remains unclear. We use budding yeast as our main model system but the Young Investigator Programme so attractive. Having access to excellent expand to mammalian systems where appropriate. At The EMBO Meeting laboratory management courses and core facilities is fantastic and provides 2015 in Birmingham I will present the work done by my group over the last essential support at this key stage of my career. The networking aspect is three years. also very appealing. I am already looking forward to meeting all the other Young Investigators at the upcoming meeting in Barcelona. You have a young family. How do you manage? Good question. It works because my lab team and my husband are flexible. And the good thing Scientific heroes. Since my early days at medical school, I have been fasci- about being a group leader is that a lot of the work can be done at home nated by the work of Eric Olson and his ability to recognize fundamental when the kids are in bed. As a postdoc it was much more difficult because mechanisms of gene regulation in complex biological phenotypes. I should the bigger part of the work was still pipetting. also mention Holger Gerhardt in this context, whose innovative approach to developmental vascular biology has always been a source of inspiration. Holger used to be an EMBO Young Investigator and he encouraged me to apply to this programme.

6 EMBOencounters | Winter 2014 | 2015 | [email protected] ©2015 EMBO news from the embo community Meet the scientist EMBO Young Investigators & Installation Grantees 2014 EMBO I ns 2014 EMBO I ns t t alla alla t ion t ion G ran t ee G ran t ee ulbenkian S cience Institute ospodářské noviny H ospodářské omáš Škoda, © T © G Pavel Plevka Ana Domingos Masaryk University, Brno, Czech Republic Gulbenkian Institute of Science, Oeiras, Portugal

Recent research. My research is focused on viruses that cause diseases in What drew you to research on obesity and eating behaviour? I became humans or are economically important pathogens of honeybees. We are fascinated by the topic when I first heard a talk by Jeffrey Friedman of the interested in honeybee viruses because they are a major factor contributing Rockefeller University before he became my postdoctoral mentor. He has to the decline of honeybee population in the European Union and United been a constant role model and valuable guide along with my PhD advisor States. The honeybee plays a vital role in the agricultural industry by provid- Leslie Vosshall. Both are unique and interesting personalities who create ing pollination services for many food crops. Moreover, abundance of wild science that can change society. For me, it has been really inspiring. In addi- insect-pollinated plant species declines in areas with reduced populations of tion to my bench work I am also committed to reaching the public. Scientific honeybees. Among human viruses, we are interested in picornaviruses that education of the the general public is the most important means of prevent- induce illnesses ranging from the common cold to life-threatening encepha- ing stigmatization and prejudice against obese patients. litis caused by enteroviruses and polioviruses. My laboratory uses a combination of crystallographic studies with cryo-electron microscopy to study Gender ratio. The gender ratio in my institute reflects the typical gender picornavirus-host interactions. ratio in the life sciences in Portugal. In our institute, 45 percent of group leaders are women, and the ratio of mothers among them is almost as high We also work on bacteriophages that could be used as antibacterial therapy as that of fathers. This comes as a surprise considering the inverse global agents. We study infection cycle of phage 812K1 that can be used as an trend in terms of gender ratio in science leadership. For specialists studying antibacterial agent to treat Staphylococcus aureus infections. Many S. aureus gender ratios in leadership, Portugal provides a lot of food for thought. strains are resistant to antibiotics and cause a range of human diseases from skin infections to life-threatening pneumonia, meningitis, and sepsis. Experience at the Rockefeller University. Rockefeller University is an Phages can be used to treat pathogenic bacteria, even those that are resistant outstanding institution. I was fortunate to spend more than a decade there to antibiotics. Structural description of the phage-bacteria interactions may during my graduate studies as well as my postgraduate research. The allow preparation of genetically modified phages targeting new bacterial University is like a small oasis in the middle of New York city. People say strains. that good perfumes come in small packages, and I feel that Rockefeller is all about that: a university with a small campus that already gave rise to 24 Changing directions. My research interests have always been related to Nobel Laureates. A small campus like this facilitates human and scientific viruses. From the time I entered university I was intrigued by virology and interactions that can lead to groundbreaking research. molecular biology. During my pre- and post-doctoral studies I worked on virus-related projects ranging from bacteriophages and plant viruses to Changing directions. It happened very often. First I changed direction from mouse polyomavirus and viruses causing disease in humans. However, I an undergraduate degree in pencil-and-paper mathematics (not applied have changed the methodological approaches from molecular and cell biol- mathematics) to a PhD in “wet” neurobiology of olfaction in Drosophila. As ogy methods to X-ray crystallography and electron microscopy. a postdoctoral researcher, I switched to research in neurobiology of obesity, using mice as a model system. Currently I am dipping my fingers in Research in the United States. Working with Michael Rossmann at Purdue immunology. Obesity involves malfunction of multiple systems and organs University was a stimulating experience. The team was very international – I think of it as a systems level disease. We need to have an integrative – it included at least seven nationalities. I am striving to emulate a similar approach to understand what goes wrong, and that will require a multidis- environment in my laboratory. The Czech scientific environment is quite ciplinary effort. different to the United States for historical reasons. Diversity and mobility of researchers are limited but the situation is improving. In the structural Initial collaborations after coming back to Portugal. First I established biology research program of CEITEC (my home institute) all new research collaborations locally and now I am counting on the EMBO network to group leaders have experience from abroad or are foreigners. expand them. I already touched base with some scientists from the network but it is still too early to know if this will work. I am optimistic. Challenges in setting up my own group. I face four major challenges: secur- ing research funding, recruiting capable team members, establishing functional collaborations, and training PhD students and postdoctoral researchers in my group. Perhaps it is balancing all the requirements that is most challenging.

©2015 EMBO EMBOencounters | Winter 2014 | 2015 | [email protected] 7 interview We need a CERN for genomics Emmanouil Dermitzakis is currently the Louis-Jeantet Professor of Genetics at the University of Geneva. From 2004-2009, he was a group leader at the Wellcome Trust Sanger Institute in Cambridge. His research focuses on the genetic basis of cellular phenotypes and complex traits. In an interview with Thomas Lemberger, chief editor of the journal Molecular Systems Biology, he talks about the functional use of population genomics, disease biology and the power and challenges of large-scale sequencing projects.

Why is it important to sequence more and more Speaking about the scientific process in individual human genomes? genomics: research in genomics often involves We should sequence everybody. In fact, people large consortia. Do you think we need a CERN- should be sequenced at birth. Not because this like structure for genomics? will predict a disease. The reason is that each We need large consortia because the major efforts one of us is going to have something that is need to be done collectively – compiling the data, rare or even private. To better understand a rare deciding on standards, organising and sharing condition it is always helpful if you compare to available data. Establishing a homogenous way other patients without that mutation. It will also to do all these things has helped genomics very Your research focuses on understanding the improve our understanding of the impact of the much. On the other hand, innovation will not genomic basis of human variation. What is your DNA sequence on particular phenotypes. Some come from consortia. Consortia are just helping general approach? to build a base line that people can step on and Studying variation in humans touches both basic move on to discover interesting things. We need science and medically related questions dealing “I think everybody should be a mix of both. In my opinion we do need a CERN with disease, treatment and the understanding for genomics for two reasons. First of all we of disease in general. Our approach is from a sequenced because it is a funda- need structures in Europe that will influence the basic perspective. We are trying to understand mental thing. This is similar to European setting. What we also need is a place how genetic variation in general – meaning all to meet. Because CERN is not just about doing the variants in the human population – has an looking at yourself in a mirror, research. It is also a meeting point for scientists. impact on cellular processes. weighing yourself or measuring EMBL has fulfilled this role for molecular biology. Genomics is a new revolution and we need Conducting genetic experiments is possible in your height.” to build something similar now. mice but impossible in humans. So what is the critical advantage of studying genomic variants Is it important to share findings and data prior in humans at the level of entire populations? people might be able to control it just by chang- to publication, posting the manuscripts on The advantage is not as much scientific as it is ing their behaviour as opposed to drug treatment. bioRxiv (bio-archive) for example? social. I think the interest in understanding medi- I think everybody should be sequenced because it I am split on this. My group has always been cally related questions has opened up a lot of is a fundamental thing. This is similar to looking very open about announcing things at confer- doors both on the hospital side as well as at the at yourself in a mirror, weighing yourself or meas- ences and in talks on unpublished data. I really level of the individual citizen. Sampling tissues uring your height. It would be a great benefit to like sharing data, information and discovery. But from individuals in a non-invasive way is more humanity if we reached the level where we can I am worried about the gossip. Publication, with and more accepted. We can look at cells and share DNA information without being afraid that all its caveats and its disadvantages, is an organ- generate cell lines, which serve as models to do somebody will take advantage of it. It might be ised way of sharing information. You cannot start experiments on. In fact, we do plenty of experi- difficult but we should aim for that. sharing findings and data in an aggressive way. ments on cell lines. The community needs to mature first. And we Sequencing has become very cheap, which need to be more organised about sharing infor- How do you address the often complex explains why we can sequence more and more mation, particularly publication. mechanisms that lead to a disease? people. Is it going hand in hand with similar There are two aspects to this issue: how you get a efforts to measure molecular and clinical particular disease and how you approach its treat- phenotypes? ment are two different things. One example is Phenotyping of individuals in a medical setting, diabetes that results from loss of control of glyce- so called clinical phenotypes, and the recording mia. The causes of the disease are probably long- of those phenotypes in an electronic health record term. It is a combination of genetics and envi- in an organised fashion is not very advanced. It is ronment. You cannot just reverse the causes and disappointing that now that the genome is avail- treat the disease. Because if you could, you would able we have to wait for the electronic health just lose weight and be fine again. Understanding record. It would have been great if those records the causes and informing people how to prevent were already organised. It is late to do it now a disease – called preventive medicine – is one because every hospital has its own system and thing. But treating a patient who lost the equilib- in addition the national health systems are often rium is a whole different approach. totally different.

Academic research is clearly a driving force in this project but it is also relevant to industry. Companies and scientific institutes are working increasingly together to develop new and upgrade existing microscopes that will speed up innovation in Europe. The recently launched Euro- BioImaging Industry Board aims to bring imaging companies in Europe closer to this infrastructure. In the times of economic austerity, biotech and pharmaceutical companies are reducing budgets for R&D and are becoming increasingly interested in shared resources.

Ensuring Europe’s competitiveness “Europe is quite competitive in biological and medical imaging research, and must remain so in the future,” says Jason Swedlow, Professor at the University of Dundee. New innovative imaging technologies were born here – one of the most recent was developed by Stefan Hell, who was awarded the Nobel Prize in Chemistry last year. Another European asset is a strong network of software developers working on the next genera- Euro-BioImaging tion of data processing tools for imaging. And thanks to the launch of the Euro-BioImaging Open Access infrastructure for imaging technologies project five years ago, new national imaging hotolab EMBL communities have opened and are actively oper- © P ating in 25 European countries. Bioimaging has been declared a national priority in twelve EU countries. RET stands for Fluorescence Resonance project officer at EMBL. Bottlenecks mainly occur Inna Ulyakina from the University of Lisbon is Energy Transfer and describes a micros- in providing highly demanding and challenging one of the visiting scientists who used the high- Fcopy technique used to visualise processes technologies such as super resolution, function- throughput content light microscopy at EMBL’s in individual cells, such as protein–protein or al imaging or correlative imaging that are only Advanced Light Microscopy Facility. She was able protein–DNA interactions. The technique is not offered by a small number of institutes, but are in to identify novel therapeutic compounds for cyst- new, but it is complex and requires years of exper- huge demand by a large number of scientists in ic fibrosis and the results of the study were finally tise. The demand from the scientific community Europe and worldwide. published in a Cell paper in 2013. “It is important to use this powerful tool has been unflagging. to have a new pan-European infrastructure to be Bio-imaging techniques such as FRET and able to perform high quality research using the other functional imaging techniques, for exam- best available technologies and having profes- ple super resolution, high content screening sional support for the assay development, data or Correlative Light and Electron Microscopy processing and analysis,” she says. (CLEM), have experienced phenomenal growth After the five-year preparatory phase finished within the last decades. However, these tech- in 2014, the project was handed over from the nologies are costly and require very high level scientific community to the research ministries of expertise to run them. Many European life that will now decide which centres may join the scientists lack access to such innovative imaging infrastructure and receive the needed financial technologies and this can slow down scientific upgrade. The funding for the nodes will come discovery. from the respective Member States, and, in some © Mayumi Isokane, EMBL In 2010, EMBL and 38 research institutes cases, countries can use European Union funds. joined forces to create a pan-European infrastruc- The nodes and the hub Currently, thirteen countries and EMBL have ture called Euro-BioImaging. Its aim is to facilitate The model is simple. The platform will be signed the Memorandum of Understanding. access to innovative imaging technologies in the composed of imaging facilities – nodes – distrib- The opportunities for discovery based on biological and medical fields. “Euro-BioImaging uted in a geographically balanced way through- microscopy are enormous: imaging could provide will provide access to the latest equipment at out Europe to keep costs and time involved at the basis for novel applications across many a reasonable cost and distance,” says EMBO bay. Research centres from 19 European coun- biological and biomedical sciences. One exam- Member Jan Ellenberg, who was the scientific tries have already submitted written expressions ple could be linking spatial and temporal scales coordinator of the Preparatory Phase coordinated of interest in becoming such a node. Nodes will by combining different approaches to imaging. by EMBL. “All European scientists should have be accessible to European and international A promising technique to achieve this is to link access to the full range of advanced, innovative researchers, and experts working there will MRI or X-ray images of whole plants, animals or imaging technologies including the instruments, support them through all steps of their imaging humans with the molecular specificity and reso- handling and processing of data, and converting experiments. A European hub, where strategic lution afforded by light and electron microscopy it into publishable results.” and financial decisions are made, will coordinate – a method that could bring about improvements The growing need for service, training and the services offered by the nodes. The call for the in both diagnosis and therapy. technology infrastructure poses capacity problems countries that wish to host the hub and provide for many research centres. “We are hitting our legal personality to Euro-BioImaging was opened www.eurobioimaging.eu/ limits,” admits Tanja Ninkovic, Euro-BioImaging last January.

The EMBO building plunged into darkness on the first evening of the Members’ Meeting held last October. A slideshow of The EMBO Journal cover images framed the welcome reception attended by more than a hundred guests (left). An audiovisual performance in the ATC auditorium was one of the highlights (above). © Pictures: P hotolab EMBL

50th Anniversary EMBO Members’ Meeting

MBO celebrated its 50th anniversary with On the occasion of its 50th anniversary, EMBO The meeting was a wonderful occasion for a series of inspiring activities and events decided to enlarge its membership to include new and established members to meet their Ethroughout 2014. The EMBO-EMBL Science more researchers who work in the areas of colleagues and to celebrate the organisation and and Policy Meeting held in July to celebrate neuroscience, ecology and evolution. The new the people who made EMBO what it is today. the anniversaries of EMBO, EMBL and EMBC members selected in the anniversary year and in More than 120 guests enjoyed three days filled was followed by the FEBS-EMBO Anniversary 2013 were invited to present their latest research with scientific talks and creative entertainment Conference held in Paris in September 2014. The and discuss the role of EMBO in furthering the featuring a molecular gala dinner and an experi- festivities culminated in a central event for all latest science. mental audiovisual performance. EMBO Members held in October in Heidelberg.

50th Anniversary EMBO Members Finding one’s own Meeting 2014 name on the carpet showing the names of 1650 Members was a challenging MENU task (below). MOLECULAR CUISINE Day two culminated FOR in a molecular dinner featuring Professor of Molecular Gastronomy Peter Barham shown live from the United MOLECULAR Kingdom. BIOLOGISTS

The guests created their own dessert – a vanilla ice-cream – by using liquid nitrogen

Parents help find diagnosis for

rare disease Matt Wilsey (front left), Kristen Wilsey (front right), EMBO Associate Member Shinya Yamanaka EMBO Member Lars Steinmetz and Associate Member Shinya (front, second left) and colleagues. Yamanaka are part of an international team trying to find a solution for a rare disease that was first diagnosed thanks to the efforts of the deficiency, the Wilsey’s established the Grace parents of affected children. Wilsey Foundation (gracewilsey.org), which is led by people from science, medicine, business, and the public service. The foundation helps to coordinate fundraising. The Wilsey’s have also provided significant personal financial support disease or disorder is defined as rare in Co-director of the Stanford Genome Technology for the research. Today a scientific team of glyco- Europe when it affects fewer than 1 in Center, who is working on the project. “When biologists, cell biologists, biochemical geneticists, A2000. In the United States it has to affect this enzyme is defective you could get an accu- chemists and experts in gene therapy are working fewer than 200, 000 Americans at any given time. mulation of protein aggregates in cells. However, on the project. Grace Wilsey was a huge puzzle to her parents NGLY1 could also be involved in other functions.” It has been a long path for the parents to and doctors after she was born. At the age of 4 For NGLY1 deficiency to arise, a person needs reach a point where they have a diagnosis for the months onwards her development was delayed, to inherit two faulty copies of the gene from his disease and some understanding of what goes but initial diagnostic tests gave no clear answer or her parents (autosomal recessive disorder). wrong in the cells of patients. No one is under about the cause of the problems. Whatever condi- The condition affects a degradation pathway that any illusion that the journey towards a cure tion she had seemed to affect every organ in her takes place within the endoplasmic reticulum will be straightforward. What is needed now is body. What followed were visits from one doctor of cells in such a way that it leads to neurologi- a concerted effort to understand the molecular to another, incorrect diagnoses, tests and further cal dysfunction, abnormal tear production, and events that arise from NGLY1 deficiency and to tests. Frustrated by the lack of interest from the liver disease. NGLY1 deficiency patients show identify possible intervention points where new pharmaceutical industry as well as uncertainty global developmental delay, movement disor- therapeutics or treatments would make sense. from the medical community the parents of Grace der, and low muscle tone (hypotonia). Other This is where the work of Steinmetz, Yamanaka set out to involve others in finding a solution. common symptoms include elevated levels of and other members of the team that the Wilsey’s Things started to fall into place about the liver transaminase enzymes, reduced head size have put together hope to make contributions. cause of the disease after a small group of (microcephaly), diminished reflexes and seizures. “We are now trying to find out why deficien- patients was identified. One of the crucial pieces “NGLY1 happens to be a very central part of cies in the NGLY1 gene cause many of the symp- of evidence arose from whole genome sequenc- cellular metabolism and it is going to be linked toms of these children and we are trying to find a ing for Grace (other patients had their whole to a lot more types of disorders as we work out cure,” says Yamanaka. “We still need to do a lot exome sequenced), which confirmed that those what it is doing,” says Dr Gregory Enns, Director of basic research to do this and also to find out affected had defective copies of the NGLY1 gene. of the Biochemical Genetics Program at Stanford how frequent the disease is. At this point in time, Another crucial clinical observation was a lack of University. Much of the work that led to the diag- we just do not know.” tears in patients. nosis has been written up in a paper published It turns out the NGLY1 gene encodes an in Genetics in Medicine.* Enns wrote the paper *Enns G, Shashi V and Bainbridge M (2014) Mutations in enzyme that removes a sugar molecule from that included input from thirty-three authors NGLY1 cause an inherited disorder of the endoplasmic damaged proteins. “What is known is that NGLY1 from four countries around the world. The paper reticulum–associated degradation pathway. Genetics in Medicine 16: 751–758. helps to get rid of misfolded proteins in cells,” says describes the DNA sequencing work and the find- Steinmetz, Associate Head of Genome Biology ings from the study of eight patients. & Senior Scientist at the European Molecular “The parents really spearheaded putting Biology Laboratory in Heidelberg, Germany, the international team of scientists together,” Professor of Genetics at Stanford University and says Steinmetz. To further the work on NGLY1

12 EMBOencounters | Winter 2014 | 2015 | [email protected] ©2015 EMBO The goals are to help inform both patients and researchers about a disease for which any one Teenager discovers a possible institution only has a small about of data. The genetic data from the tumours of 15 patients were obtained for the fibrolamellar cause for her own cancer cancer project. It turned out that all 15 patients “When I was diagnosed with fibrolamellar cancer, it seemed like few shared a piece of DNA that had been broken and joined back together in a way that created a people knew much about the disease,” says Elana Simon who was 12 mutant gene or “chimera.” During this fracture- years old at the time. “No one knew much about what to do with it.” fusion process a 400-kilobase sequence of DNA on chromosome 19 is removed. The mutant gene that resulted was not present in the tissue of healthy individuals. This DNA deletion most likely creates “unnatural proteins” that can drive the onset and progress of fibrolamellar cancer. ibrolamellar hepatocellular carcinoma is a father, Sandy Simon, professor and head of The results of the study have been published rare liver tumour that affects adolescents the Laboratory of Cellular Biophysics at the in a paper that appeared in Science early last Fand young adults who have no history of Rockefeller University, since she wanted to be year.* Elana, now a 19-year-old student study- liver disease. The standard treatment is removal independent. However, the possibility of pursu- ing computer science at Harvard University, is of the tumour by surgery. Little is known about ing her dream took precedence over independ- one of the lead authors on the paper. Sanford how the disease develops at the molecular level ence and she started working in his laboratory Simon, Elana’s father, adds: “It is uncommon for and diagnostic tests are currently unavailable. in her spare time outside of high school, together a genetic screen for a cancer to turn up such a Patients with advanced stages of the disease have with surgical fellows of Dr. LaQuaglia’s group at strong candidate mutation, and for the mutation few treatment options. After diagnosis, Elana had the Memorial Sloan-Kettering. to be present in every single patient tested.” The an operation to remove much of her liver. Four Elana and colleagues used the latest sequenc- hope now is that the molecular signature that has years after the surgery she decided to learn more ing technologies and bioinformatics tools and been discovered can be developed into an effec- about her cancer and made the bold decision to made the decision to study not just a select tive early-stage diagnostic marker of the disease. investigate her own disease. To train herself, she section of fibrolamellar DNA but her entire If successful it should be possible to screen blood samples of individuals for the tell-tale signs of cancer and make interventions at the earliest possible opportunity. Further work is in progress to see what molecular changes ensue from the observed deletion of DNA and to try and charac- terize the many molecular events that give rise to fibrolamellar hepatocellular carcinoma. On January 30, 2015, in the East Room of the White House, President Obama delivered remarks on his plan to expand precision medicine, a medical approach that will provide treatments that match the needs of individuals and which offers new ways to understand and tackle rare diseases. Elana Simon was at the event to talk about her experience and had the pleasure of introducing the President. Determination and curiosity have been essential in Elana Simon’s quest to understand her disease. “I want everyone out there

© Agency/Getty Images S amuel Corum/Anadolu with rare diseases to know that it’s really up to the patients to motivate progress and now we can took an internship in a medical school labora- genome, even though this meant far more work actually do so,” concludes Simon. tory exploring the genomics of pancreatic cancer. than usual. Together with other patients, family However, the results frustrated her. Pancreatic members, scientists, and contributors, they set *Joshua N. Honeyman, Elana P. Simon, et al. (2014) Detection cancers have thousands of single nucleotide vari- up The Fibrolamellar Tissue Repository at the of a recurrent DNAJB1-PRKACA chimeric transcript in ants because they have often been in the patient Rockefeller University. The ready availability fibrolamellar hepatocellular carcinoma. Science 6174: 1010–1014. for years before being found, giving time for of tissue samples facilitates the daily work of many mutations to accumulate. Since they occur researchers. It helps scientists build up a picture of in an older population even the normal cells the shared molecular similarities of patients with For further information: have many mutations due to the aging process. the same diseases. In many cases patients may The Fibrolamellar Cancer Foundation: www.fibrofoundation.org Elana wanted to study a paediatric cancer – her be living in very different geographic locations The Fibrolamellar Registry: own cancer – in the hope there would be fewer and communication and outreach are essential to www.fibroregistry.org mutations in the tumour cells and few mutations build an effective repository. Elana, together with The Fibrolamellar Tissue Repository: in the normal cells of the body. “When we iden- other patients, also established the Fibrolamellar fibrolamellar.rockefeller.edu tify a possible mutation in an adolescent, it is Registry, which helps provide information about President Obama speaks on the Precision much more likely to be driving the cancer,” says research for patients and is serving as a nascent Medicine Initiative: Elana. Her surgeon, Dr. Michael LaQuaglia of Patient-Owned Electronic Medical (POEM) regis- www.youtube.com/watch?v=MKiw7yAqqsU Memorial Sloan-Kettering Cancer Center, encour- try. Elana and colleagues hope to expand this to aged her, but she could not find a lab space to a full-scale medical database for the disease that work. She ignored the offer of space from her is shared with multiple groups and institutions.

Practical Courses Workshops Conferences ESF | EMBO Symposia In vivo plant imaging Emerging concepts of the neuronal Mechanisms and regulation of Bacterial Networks (BacNet 15) DE-Heidelberg, 9–15 March 2015 cytoskeleton protein translocation ES-Sant Feliu de Guixols, 9–15 May 2015 CL-Puerto Varas, 22–26 March 2015 HR-Dubrovnik, 21–25 March 2015 Single molecule and single cell Be there or die? The role of the fluorescence Å/nm/µm/mm-scopy Modern DNA concepts and tools for Chromatin and epigenetics microenvironment in B cell behaviour DE-Heidelberg, 15–23 March 2015 safe gene transfer and modification DE-Heidelberg, 6–10 May 2015 in health and disease FR-Evry, 30 March–3 April 2015 ES-Sant Feliu de Guixols, 16–21 May 2015 Advanced optical microscopy Molecular chaperones: From UK-Plymouth, 8–18 April 2015 Microbial sulfur metabolism molecules to cells and misfolding Symbiomes: Systems biology of host- DK-Helsingør, 12–15 April 2015 diseases microbiome interactions The characterization of post- GR-Heraklion, 8–13 May 2015 PL-Pułtusk, 5–10 June 2015 translational modifications Cortical development in health and DK-Odense, 9–15 April 2015 disease Europhosphatase 2015: Thiol-based redox switches in life IL-Rehovot, 26–29 April 2015 Phosphorylation switches and sciences Computational biology: From cellular homeostasis ES-Sant Feliu de Guixols, genomes to systems Embryonic-extraembryonic FI-Turku, 24–29 June 2015 12–17 September 2015 JP-Okinawa, 17–22 April 2015 interfaces: Emphasis on molecular control of development in amniotes RNA localization and local translation Interaction between the immune Single-cell gene expression analysis DE-Göttingen, 6–9 May 2015 GR-Hersonissos, 28 June–3 July 2015 system and nanomaterials: Safety DE-Heidelberg, 17–22 April 2015 and medical exploitation SMC proteins: Chromosomal Molecular and population biology PL-Pułtusk, 4–9 October 2015 Small angle neutron and X-ray organizers from bacteria to human of mosquitoes and other disease scattering from proteins in solution AT-Vienna, 12–15 May 2015 vectors: Current, resurgent and FR-Grenoble, 18–22 May 2015 emerging diseases EMBO | FEBS Lecture Courses Dynamic kinetochore GR-Kolymbari, 24–29 July 2015 Modern biophysical methods for DK-Copenhagen, 18–21 May 2015 Biomembranes: Molecular protein-ligand interactions DNA replication, chromosome architecture, dynamics and function FI-Oulu, 1–5 June 2015 Developmental circuits in aging segregation and cell division FR-Cargèse, 15–25 June 2015 GR-Hersonissos, 25–28 May 2015 UK-Egham, 27–31 July 2015 Synthetic biology in action Mitochondria in life, death and disease DE-Heidelberg, 8–20 June 2015 Cellular synapsis for cell-cell Ribosome synthesis GR-Fodele, 12–16 October 2015 signalling BE-Brussels, 19–23 August 2015 Advanced electron microscopy for cell ES-San Lorenzo del Escorial (Madrid), biology 26–29 May 2015 Aquatic microbial ecology EMBO | EMBL Symposia FR-Bordeaux, 9–18 June 2015 SE-Uppsala, 23–28 August 2015 Macromolecular assemblies at the Frontiers in stem cells and cancer The application of transient crossroads of cell stress and function Meiosis DE-Heidelberg, 29–31 March 2015 kinetic methods to biological IL-Jerusalem, 31 May–4 June 2015 UK-Oxford, 30 August–4 September 2015 macromolecules Cellular heterogeneity: Role of UK-Kent, 21–27 June 2015 Mechanisms of plant speciation Physics of cells: From molecules to variability and noise in biological SE-Norrtälje, 9–13 June 2015 systems (PhysCell 2015) decision-making Developmental neurobiology: From DE-Bad Staffelstein, 30 August– DE-Heidelberg, 15–18 April 2015 worms to mammals Cell biology of animal lectins 4 September 2015 UK-London, 21 June–4 July 2015 IL-Rehovot, 21–25 June 2015 Mechanisms of neurodegeneration Autophagy signalling and progression DE-Heidelberg, 14–17 June 2015 High-throughput protein production Cortical interneurons in health and in health and disease and crystallization disease IT-Chia, 9–12 September 2015 Enabling technologies for eukaryotic FR-Marseille, 29 June–8 July 2015 ES-Costa d´En Blanes (Mallorca), synthetic biology 22–25 June 2015 Cell therapy today: Achievements, DE-Heidelberg, 21–23 June 2015 Marine animal models in evolution hopes and hypes and development Neural circuits and behaviour of UK-Manchester, 9–12 September 2015 The mobile genome: Genetic and SE-Fiskebäckskil, 5–18 July 2015 Drosophila physiological impacts of transposable GR-Kolymbari, 5–10 July 2015 Protein synthesis and translational elements Multi-level modelling of control DE-Heidelberg, 16–19 September 2015 morphogenesis Cellular and molecular mechanism of DE-Heidelberg, 9–13 September 2015 UK-Norwich, 12–24 July 2015 tumour–microenvironment crosstalk Seeing is believing: Imaging the RU-Tomsk, 9–12 July 2015 Ubiquitin and ubiquitin-like processes of life Analysis of small non-coding RNAs: modifiers: From molecular DE-Heidelberg, 6–10 October 2015 Per aspera ad astra Cell and developmental systems mechanisms to human diseases CZ-Brno, 25–31 July 2015 CH-Arolla, 18–22 August 2015 HR-Cavtat, 18–22 September 2015 New approaches and concepts in microbiology Measuring intra-species diversity Cell cycle Signalling in plant development DE-Heidelberg, 11–14 October 2015 using high-throughput sequencing HU-Budapest, 4–7 September 2015 CZ-Brno, 20–24 September 2015 PT-Oeiras, 27–31 July 2015 Mitochondria, apoptosis and cancer Nuclear receptors: From molecules Structure, dynamics and function of (MAC 2015) EMBO Global Exhange to humans Lecture Courses biomacromolecules by solution NMR DE-Frankfurt, 10–12 September 2015 FR-Ajaccio, 24–28 September 2015 DE-Garching, 31 July–7 August 2015 Structural and biophysical methods DNA topoisomerases, DNA topology The multidisciplinary era of endocytic for biological macromolecules in Image processing for cryo electron and human health mechanics and functions solution microscopy CH-Les Diablerets, 13–17 September FR-Mandelieu-la-Napoule, TW-Taipei, 4–10 May 2015 UK-London, 1–11 September 2015 2015 27 September–2 October 2015 Frontiers in innate immunity and Two-photon imaging of brain Molecular mechanisms of muscle Genetic control of development and drug discovery function: From spiny dendrites to growth and wasting in health and evolution ZA-Johannesburg, 6–11 July 2015 circuits disease FR-Paris, 29 September–2 October 2015 DE-Munich, 6–12 September 2015 CH-Ascona, 20–25 September 2015 The DNA damage response in cell Other EMBO events Insights into plant biological Mitochondrial DNA and physiology and disease processes through phenotyping neurodegeneration GR-Cape Sounio, 5–9 October 2015 EMBO Laboratory Management BE-Ghent, 13–19 September 2015 ES-Sitges, 23–25 September 2015 Courses Current methods in cell biology DE-Leimen, Various dates DE-Heidelberg, 14–22 September 2015 Organizers: Apply now for: The EMBO Meeting Computational analysis of protein- 2016 funding for courses, workshops and conferences by UK-Birmingham, 5–8 September 2015 protein interactions: From sequences 1 March and 1 August 2015 EMBO Members’ Meeting to networks Keynote lectures given by EMBO members at major DE-Heidelberg, 28–30 October 2015 UK-Norwich, 28 September–4 October international scientific meetings in 2016 by 2015 1 February, 1 June and 1 October 16th EMBO|EMBL Science and Society Conference | Emerging Analysis of high-throughput Biotechnologies – Hype, hope, and sequencing data For a complete and up-to-date list of hard reality UK-Hinxton, 19–24 October 2015 EMBO events please go to events.embo.org DE-Heidelberg , 5–6 November 2015

EMBO THE EMBO Molecular Medicine JOURNAL LRP2BP ANKS1B INTEGRATIVE ANALYSIS INJURY LDLRAP1

LRP2 LPL

Outer mucus layer Desulfovibrio

Inner mucus layer Research article Corpus callosum Bats are a possible source of the ACTIVATED STEM CELL Ebola epidemic in West Africa Autophagic ﬂux Mitochondrial Research article Metabolic rate content/activity The outbreak of Ebola in West [ATP] Molecular network identified Africa may have originated from Research article underlying autism spectrum contact between humans and virus- disorders infected bats, suggests a study led Autophagy helps fast track by researchers from the Robert stem cell activation Research article Researchers in the United States Koch-Institute in Berlin, Germany. have identified a molecular The report identifies insectivorous Researchers from Stanford Protection of the mouse gut by network that comprises many of free-tailed bats as plausible University School of Medicine mucus depends on microbes the genes previously shown to reservoirs and expands the range of have discovered a link between a contribute to autism spectrum possible Ebola virus sources to this protective mechanism used by cells The quality of the colon mucus in disorders. The findings provide a type of bats. and the activation of muscle stem mice depends on the composition map of some of the crucial protein Ebola virus disease epidemics cells. Cells use autophagy to recycle of gut microbiota, reports a interactions that contribute to are of zoonotic origin, transmitted cellular “building blocks” and Swedish-Norwegian team of autism and will help uncover novel to human populations either generate energy during times of researchers from the University of candidate genes for the disease. through contact with larger wildlife nutrient deprivation. The scientists Gothenburg and the Norwegian “We wanted to see to what or by direct contact with bats. “We report that when this protective University of Life Sciences in Oslo. extent shared molecular pathways monitored the large mammal mechanism is operational it also The work suggests that bacteria are perturbed by the diverse set populations close to the index seems to assist in the activation of in the gut affect mucus barrier of mutations linked to autism in village Meliandou in south-eastern stem cells. properties in ways that can have the hope of distilling tractable Guinea and found no evidence “Our study reveals that when implications for health and disease. information that would benefit for a concurrent outbreak,” says stem cells emerge from a quiescent “Genetically similar mice with future studies,” says Michael Fabian H. Leendertz of the Robert state there is a rapid and dramatic subtle but stable and transmissible Snyder, Professor at the Stanford Koch Institute, who led the study. change in their metabolic activity,” intestinal microbiota showed Center for Genomics and The second infection route appears says Thomas Rando Professor unexpectedly large differences in Personalized Medicine and the lead more plausible as direct contact at Stanford University School of the inner colon mucus layer. The author of the study. with bats is usual in the affected Medicine and the lead author of the composition of the gut microbiota The researchers generated their region. study. “The induction of autophagy has significant effects on mucus interactome – the whole set of Fruit bats are the commonly seems to be a critical component of properties,” says Malin E.V. interactions within a cell – using suspected Ebola virus reservoir as these metabolic shifts and allows Johansson from the University of the BioGrid database of protein previous outbreaks in Africa show. stem cells to cope with the stressful Gothenburg who led the study. and genetic interactions. “We have Yet fruit bats seem an unlikely demands for nutrients and the By sequencing the microbiota identified a specific module within source of infection, as a food-borne building blocks for the synthesis of and examining the 16S ribosomal this interactome that comprises transmission would have affected large molecules like proteins and RNA genes, the researchers 119 proteins and which shows a adults before or concurrently with DNA that arise due to the rapid discovered that two mouse colonies very strong enrichment for autism the two-year-old boy – the index growth of the cell.” maintained in two different rooms genes,” remarks Snyder. case. This suggests a source of When stem cells are activated, in the same specific pathogen-free “The module we identified which infection unrelated to food. cells experience large changes in facility had different gut microbiota. is enriched in autism genes had Another opportunity for their metabolism since they require The different mucus properties two distinct components,” says infection was a large colony of free- increased biosynthesis of proteins were recreated by transplanting the Snyder. “One of these components tailed insectivorous bats housed in and other large molecules. The microbial communities into germ- was expressed throughout a hollow tree nearby the home of scientists discovered that autophagy free mice. “After recolonisation of different regions of the brain. The the index case. Villagers reported is turned on when muscle stem germ-free mice with the different second component had enhanced that children often used to play in cells are activated. They also microbiota we observed the molecular expression in the corpus and around the tree. This may have showed that when autophagy was same structural and functional callosum. Both components of the resulted in a massive exposure to inhibited the activation of the stem differences in their mucus network interacted extensively with bats. cells was delayed. properties,” added Johansson. each other.” Investigating the Zoonotic Origin of the Induction of autophagy supports the The gut microbiota composition impairs Integrated systems analysis reveals a West African Ebola Epidemic bioenergetic demands of quiescent the colon inner mucus layer barrier molecular network underlying autism Almudena Marí Saéz, Sabrina Weiss, muscle stem cell activation Hedvig E Jakobsson, Ana M Rodríguez- spectrum disorders Kathrin Nowak et al. Anne H. Tang and Thomas A. Rando Piñeiro, André Schütte et al. Jingjing Li, Minyi Shi, Zhihai Ma et al. Read the paper: Read the paper: Read the paper: Read the paper: doi: 10.15252/emmm.201404792 doi: 10.15252/embj.201488278 doi: 10.15252/embr.201439263 doi: 10.15252/msb.20145487

©2015 EMBO EMBOencounters | Winter 2014 | 2015 | [email protected] 15 news from the embo community New systems biology institute opens in Portugal The Biosystems & Integrative Sciences Institute (BioISI) is one of the most recent research institutions in the Portuguese life science sector

strategic funding from the Portuguese Foundation Another interesting line of research focuses on for Science and Technology for its “excellent” cork oak and its symbiotic interaction with fungi, mark in a recent evaluation by the European which enable the plant to more efficiently use Science Foundation. soil nutrients, absorb water and resist pathogens. “This new facility will further boost Portugal’s The results indicate a potential use of mycorrhi- internationally renowned reputation in the zal fungi in cork oak forest nurseries on a larger life science landscape,” says EMBO Member scale. Portugal is home to the largest cork oak Margarida Amaral who coordinates BioISI. forests in the world and cork export is one of The institute will host more than one hundred the key economic pillars. The symbiotic interac- researchers with backgrounds in bioscience, tion in cork oak roots has also been subject of physics and computational sciences, making molecular studies of thousands of genes involved it a unique multidisciplinary environment. “It in the response of cork oak to mycorrhiza fungi became clear to us that only researchers with formation. different expertise can really address the funda- One of the key challenges in establishing mental questions in systems biology,” says BioISI is to actually facilitate the cooperation Amaral. “We were lucky enough to mobilize between researchers with different backgrounds enthusiastic colleagues from the areas of physics to create maximal synergies. Located on the EMBO Member Margarida Amaral and computer science who were looking for new University of Lisbon, Faculty of Sciences campus, © Margarida Amaral challenges in biology.” BioISI frequently interacts with the faculty of the ocated on the campus of the Faculty of Major flagship projects in biosciences include mathematics and chemistry departments. BioISI Sciences of the University of Lisbon, the research on crop improvement for cork oak and also cooperates with the National Health Institute Lcentre officially started at the beginning grapevine and also on diseases such as autism (INSA) and the UniNorte consortium to explore of 2015 as a result of a merger of three research and cystic fibrosis. In a recent project, scientists the challenges of Horizon 2020, create regional facilities. The focus of its eight research groups from BioISI in collaboration with two clinicians strategies and smart specialization. It also runs comprising more than a hundred scientists is from a hospital in Valencia pre-clinically tested a multidisciplinary PhD programme in Systems to solve challenges in biology and medicine the repurposing of a new drug for cystic fibrosis Biology (“BioSys”). A programme for postdoc- through a systems biology approach. The centre patients with very rare mutations. The drug is toral fellows will start soon. has attracted around 2.2 million Euros a year expected to be approved in the United States and of external annual funding and also received in the European Union soon. www.fc.ul.pt/pt/unidade/bioisi

can be used to make the reprogramming process International consortium reveals more efficient. “I truly believe you can say we cracked the reprogramming of the cell reprogramming of the cell,” says Dr. Heck, Professor of Biomolecular Mass Spectrometry EMBO Member Albert Heck has as part of an international consortium and Proteomics at Utrecht University. Dr. Andreas Nagy from the University of revealed the molecular events underlying the reprogramming of specialized Toronto provided overall coordination of the cells to stem cells project. Thomas Preiss of the Australian National University led the RNA biology investigations and he researchers have shown how cells cells, which can give rise to almost all types of Dr. Jeong-Sun Seo of Seoul National University change their signature from specialized known cells, can also be regenerated from mature led the epigenetic studies. Tcells, for example those found in the skin cells. The researchers of Project Grandiose The researchers generated extensive tran- (fibroblasts) to stem cells, and established a blue- were able to catalogue all of the major biologi- scriptomic, epigenomic and proteomic data sets print for the molecular events involved in cellular cal checkpoints in this reprogramming process, describing the reprogramming routes leading reprogramming. The work has so far led to five which takes place in about three weeks. This from mouse embryonic fibroblasts to induced publications published on the same day in Nature included identifying which combination of genes pluripotency, the point where a cell is capable of and Nature Communications at the end of last and proteins, as well as the modified versions of generating all the cell types in the adult organism. year. The five publications are part of an inter- these genes and proteins, were associated with The data provide a comprehensive molecular national collaboration called Project Grandiose each step. A new type of stem cells, which they description of the reprogramming routes and are overseen by Andras Nagy at Mount Sinai Hospital term fuzzy or F-class stem cells, was also discov- accessible through the Project Grandiose portal in Toronto, Canada. In addition to the proteom- ered. F-class stem cells have the advantage that www.stemformatics.org 1,2 ics expertise provided by Dr. Heck’s group, the they can be produced more economically and in project includes contributions from experts in very large quantities compared to embryonic-like 1. hussein et al (2014) Genome-wide characterization of the cellular reprogramming, epigenetics, and RNA stem cells. They offer opportunities to speed up routes to pluripotency. Nature 516: 198–206. biology from laboratories in Canada, South Korea drug screening efforts, provide new possibili- 2. Benevento et al (2014) Proteome adaptation in cell reprogramming proceeds via distinct transcriptional networks. and Australia. ties to model disease and, in time, could lead to Nature Communications 5: 5613 Since Shinya Yamanaka’s groundbreaking the development of new treatments for different work, researchers know that pluripotent stem illnesses. Moreover, the data are a resource that

The new research neuropsychologists, social workers, and specially building opens up excit- trained staff. In ISD’s Memory Clinic, patients ing opportunities for and individuals at risk receive comprehensive New research centre interdisciplinary research diagnostic workup and counselling. strategies ranging from The scientists at the DZNE study neurodegen- for stroke, dementia biophysics to patient erative diseases such as Alzheimer’s disease, fron- oriented research. While totemporal dementia (FTD), amyotrophic lateral and neurodegenerative in the past the research sclerosis (ALS) and Parkinson’s disease. They teams of the DZNE were investigate their causes and novel approaches to based in many different prevention and therapy, including new health- diseases locations on the Munich care strategies. DZNE research ranges from the university campus, they study of molecular processes in simple organisms Opportunities to link disease-oriented basic are now able to work and brain cells to human clinical trials, popula- science with clinical research hand in hand with their tion studies and healthcare research. colleagues at the ISD, EMBO Member Christian Haass, a renowned which is situated next researcher who studies dementia, has been s individuals get older, many people report door. The idea behind the move is to tightly appointed as speaker of the DZNE. Haass and a decline of cognitive skills. The number link disease-oriented basic science with clinical his colleagues are interested in the cellular and Aof people with dementia is estimated to research in an attempt to develop new diagnos- genetic mechanisms linked to different neuro- increase to more than 80 million by 2040. In tic and therapeutic options for neurodegenerative degenerative diseases. “In our laboratories, we Europe, more than 5 million people suffer from diseases. focus for example on the cellular mechanisms of dementia disorders. Like dementia, stroke ranks Both institutes differ considerably in their neurodegeneration. We believe that protein depo- among the ten most frequent diseases worldwide scientific approach. At the ISD, the basic idea sition and clearance of amyloidogenic peptides is and the most pressing health problems in ageing is to integrate patient care with clinical and mediated by common general mechanisms.” societies (WHO World Health Report 2002). To basic research to change medicine. The institute, Munich is one of nine DZNE sites located all further strengthen and concentrate the research headed by Martin Dichgans, is designed as a over Germany. The DZNE closely cooperates with on dementia and stroke in Munich, Germany, two novel type of research facility bridging the tradi- the two Munich universities, their clinics and leading institutions in these fields were recently tional barriers between academic medicine and with other research institutions in the region. The combined under one roof: the Institute for Stroke basic science. Patient care involves prevention, Biochemistry Department of the Medical Faculty and Dementia Research (ISD) and the Munich diagnosis and treatment of stroke and cognitive of the Ludwig Maximilian University, which is site of the German Center for Neurodegenerative decline. Outpatient services at ISD are provided also headed by Haass, also moved into the new Diseases (DZNE). by board certified neurologists and psychiatrists, research building.

Stem cell highlights for high schoolers Courses for 12–14 year olds on the essential concepts, applications and ethics of stem cell biology

esearchers are often enthusiastic about outreach to high-school students but lack the time to prepare lessons or imple- uro S temCell R © E ment them in a school setting. EMBO Member Ian Chambers from the University of Edinburgh learning process were eventually described in the development workshops using these lessons as developed a popular series of lessons for 12–14 January 2015 issue of the journal EMBO reports. an example. The Guardian rated them as a “top year olds that has been widely used in schools (http://embor.embopress.org/content/16/1/7) resource” and made them available on its website. and other training events throughout Europe and The article offers guidance and advice for all (http://tinyurl.com/139uaav) beyond. The three lessons focused on the essen- scientists interested in developing similar educa- It all started with an email: The idea to devel- tial concepts, applications for regenerative medi- tional modules. The authors list critical points op creative and fun lessons for school children cine and the ethical implications of developing such as paying attention to the curriculum and was triggered by the head teacher of Chambers’ stem cell treatments. They are available online at setting clear learning objectives, using a modu- old high school, The Derby School in Edinburgh. www.eurostemcell.org in five different languages. lar format for flexibility and ease of translation She found out that the professor’s interest in Chambers teamed up with Emma Kemp, a and building a relationship with the teachers. At science was sparked off during an open day visit science communicator for EuroStemCell, to the end of the three-year learning process, the at the local university at the age of 13. So she develop this tool. “Our motivation was to reach lessons had been delivered to approximately 700 invited him to give a talk about stem cell science those who would not choose science as their students by six researchers. 300 print kits of the at his old school. Developing full-fledged educa- career,” says Chambers. “Engaging these students first lesson have been distributed to educators tional modules and rolling them out to hundreds is essential to enhance the general level of scien- and scientists all over Europe and more than 250 of students and science teachers across Europe tific literacy in society.” Their experience and the European science teachers attended professional were natural next steps.

2015 Breakthrough Prize them extremely vulnerable to infections. He on and off.” The prizes are awarded by Richard Lounsbery Award Emmanuelle Charpentier of the Helmholtz has received the prize and a cash award of the University of Oslo and are among the Frédéric Saudou of the Grenoble Institute Centre for Infection Research and the approximately 416,600 US dollars together most important within Nordic biomedical of Neuroscience was awarded the 2014 research. Laboratory for Molecular Infection with Theodore Friedmann of the University Richard Lounsbery Award for 2014. The Medicine Sweden (EMBL Nordic Node in of California San Diego. Helmholtz International Fellow Award 50,000 US dollar prize is given in alternate Molecular Medicine) is one of the winners Emil von Behring Prize years to young French and American scien- of the Breakthrough Prize in Life Sciences The British cell biologist Amanda Gay tists by the National Academy of Sciences this year. She received it together with Stewart Cole has been awarded the 2014 Fisher of Imperial College London has been or the French Académie des Sciences. Jennifer Doudna for their revolution- Emil von Behring Prize from the University honored with the Helmholtz International Saudou received the award “for his major ary work on CRISPR-Cas9. Since their of Marburg for his contributions to the Fellow Award for her research. Fisher is contributions to the understanding of one of seven outstanding researchers from groundbreaking research on genome field of tuberculosis. He is being recognized molecular and cellular mechanisms causing abroad who received the award, each of editing in 2012, the CRISPR-Cas9 system “for his outstanding work in the field of Huntington’s disease. His findings represent which is endowed with 20,000 Euros. is now used by research groups worldwide tuberculosis research,” which includes a seminal discovery in the understanding of for applications in disease diagnosis and groundbreaking publications on the genom- Avery-Landsteiner-Award Huntington’s disease and an important step treatment, medical therapeutics and ics of Mycobacterium tuberculosis and towards a future therapeutic strategy.” bioenergy. The Breakthrough Prize, which Mycobacterium leprae. The Emil von Behring Andreas Radbruch of the German is worth 3 million US dollars, is sponsored, Prize is awarded every two years by the Rheumatism Research Center in Berlin 2015 Women in Cell Biology Early among others, by internet entrepreneurs University of Marburg to honour scientific has been awarded the Avery-Landsteiner- Career Medal Mark Zuckerberg of Facebook and Sergey achievements in medical, veterinary and Award 2014 of the German Society for Victoria Cowling of the University of Brin of Google. scientific areas, with an emphasis on Immunology. The 10,000 Euro prize is Dundee has been awarded the Women in immunology and disease control. awarded every two years to outstanding Louis-Jeantet Prize for Medicine immunologists. Cell Biology Early Career Medal from the Thomas Hunt Morgan Medal British Society of Cell Biology (BSCB) for Emmanuelle Charpentier is also the French Academy of Science 2015. The WICB Early Career Medal has recipient of the 2015 Louis-Jeantet Prize for Brian Charlesworth (University of been established this year to mark the Medicine for her contribution to harnessing Edinburgh) has been awarded the Thomas Olivier Voinnet of the ETH Zurich has been 50th anniversary of the founding of the an ancient mechanism of bacterial immu- Hunt Morgan Medal from the Genetics elected to the French Academy of Science in BSCB. It will be awarded to an outstanding nity into a powerful technology for editing Society of America for lifetime achieve- December 2014. female cell biologist who has started their genomes. She wins the prize together with ment in the field of genetics. The award own research group in the United Kingdom the Austrian scientist Rudolf Zechner. Each recognizes his extraordinary impact on our French Academy of Science Award within the last seven years. award is worth 700,000 Swiss Francs. understanding of population genetics and Shahragim Tajbakhsh of the Pasteur evolutionary biology. Institute, France, was awarded the French Japan Prize Academy of Sciences award for work on Alain Fischer, director of immunology at Anders Jahre’s Award for Medical stem cell research in October 2014. The the Necker Hospital in Paris, France, was Research prize comes with an award of 50,000 Euros. Congratulations to EMBO Members, Young named one of the three recipients of the Kristian Helin of the University of Investigators and Installation Grantees 2015 Japan Prize, a prestigious internation- Copenhagen received the Anders Jahre’s Academy of Athens who received this year’s Starting Grants al award. Fischer is credited with demon- Award for Medical Research in 2014 “for Nektarios Tavernarakis of the University of awarded by the European Research Council. strating the clinical efficacy of gene therapy his groundbreaking contributions to under- Crete Medical School has been awarded the The full list of names can be found at by successfully treating children suffering stand epigenetics – chemical modifications BioMedical Research Prize of the Academy http://erc.europa.eu/media-and-events/ from a severe genetic disorder that renders of our genetic material that turn genes of Athens in 2014. press-releases/2014

Books A good read – Publications from the EMBO Community embo members, Young Investigators & Fellows Life’s Blueprint: The science and art of Mouse tetrad analysis provides SLC38A9 is a component of the Combining in-cell NMR and X-ray embryo creation insights into recombination lysosomal amino acid sensing fluorescence microscopy to reveal mechanisms and hotspot machinery that controls mTORC1 the intracellular maturation states Benny Shilo (EMBO Member) evolutionary dynamics Giulio Superti-Furga (EMBO Member), of human superoxide dismutase 1 Yale University Press | Bernhard de Massy (EMBO Member) Claudine Kraft (EMBO Young Lucia Banci (EMBO Member) and October 2014 and colleagues Investigator), Richard K. Kandasamy colleagues ISBN: 9780300196634 Nature Genetics | 24 August 2014 (EMBO Fellow) and colleagues Chemical Communications | 13 November 2014 doi: 10.1038/ng.3068 Nature | 7 January 2015 doi: 10.1039/C4CC08129C http://shilobook.weizmann.ac.il/?page_id=65 doi: 10.1038/nature14107 Sequence composition of disordered Origins and functional consequences regions fine-tunes protein half-life Spatiotemporal transcriptomics of somatic mitochondrial DNA From a pinch of salt to the ribosome. M Madan Babu (EMBO Young reveals the evolutionary history of mutations in human cancer The history of crystallography as seen through the Investigator), Sreenivas Chavali (EMBO the endoderm germ layer Young Seok Ju (EMBO Fellow), Michael lens of the Nobel Prize Fellow) and colleagues Itai Yanai (EMBO Young Investigator) Stratton (EMBO Member) and Nature Structural & Molecular Biology | and colleagues colleagues Edited by: Ivar Olofsson, Sven Lidin and 2 February 2015 Nature | 10 December 2014 eLife | 1 October 2014 Anders Liljas (EMBO Member) doi:10.1038/nsmb.2958 doi: 10.1038/nature13996 doi: 10.7554/eLife.02935 World Scientific | December 2014 Genomic profiling of DNA In-cell NMR reveals potential Extensive transduction of non ISBN: 978-981-4623-11-7 methyltransferases reveals a role for precursor of toxic species from SOD1 repetitive DNA mediated by L1 DNMT3B in genic methylation fALS mutants retrotransposition in cancer Tuncay Baubec (EMBO Fellow), Dirk genomes Microbial Biochemistry Lucia Banci (EMBO Member) and Schübeler (EMBO Member) and colleagues Young Seok Ju (EMBO Fellow), Michael (2nd ed.) colleagues Nature Communications | Stratton (EMBO Member) and Georges Cohen (EMBO Member) Nature | 21 January 2015 27 November 2014 colleagues doi: 10.1038/nature14176 doi: 10.1038/ncomms6502 Science | August 2014 Springer doi: 10.1126/science.1251343 Computational analysis of cell-to- In vivo imaging of Nematostella ISBN 978-90-481-9437-7 Cell | 7 November 2013 cell heterogeneity in single-cell vectensis embryogenesis and late doi: 10.1016/j.cell.2013.10.001 RNA-sequencing data reveals hidden development using fluorescent Metallomics and the Cell subpopulations of cells probes Series Metal Ions in Life Sarah Teichmann (EMBO Member), Timothy DuBuc (EMBO Short-Term Sciences Vol. 12 Florian Buettner (EMBO Short-Term Fellow) and colleagues Fellow) and colleagues BMC Cell Biology | 2014 Lucia Banci (EMBO Member) Nature Biotechnology | 19 January 2015 doi: 10.1186/s12860-014-0044-2 Springer doi: 10.1038/nbt.3102 ISBN: 978-94-007-5561-1

Young Investigators 2014 Gad Asher Michael Hothorn lionel Navarro Maria Teresa Teixeira Mammalian circadian clocks Membrane signalling in plants small RNAs and innate immunity Telomere biology IL Weizmann Institute of Science CH University of Geneva FR Institute of Biology of the ENS (IBENS) FR Laboratory of Molecular and Cellular Biology of Eukaryotes, IBPC petr Broz Jan Huisken Caren Norden Inflammasome complexes Imaging developmental processes Retinal morphogenesis Kristin Tessmar-Raible CH Biocentre, University of Basel DE Max-Planck-Institute of Molecular DE Max-Planck-Institute of Molecular Circalunar clocks Cell Biology and Genetics Cell Biology and Genetics AT Max F. Perutz Laboratories Felipe Cortés Ledesma Repair of blocked DNA breaks Claudine Kraft Diego Pasini Ines Thiele ES Andalusian Molecular Biology Regulation and signalling in autophagy Epigenetics in differentiation and cancer Modelling of human metabolism and Regenerative Medicine Centre AT Max F. Perutz Laboratories IT European Institute of Oncology (IEO) LU Luxembourg Centre for Systems Biomedicine, University of Luxembourg Filippo Del Bene François Leulier lori Passmore Neural circuit formation and function host/microbiota interactions Macromolecular machines for RNA Steven West FR Institute Curie FR Institute of Functional Genomics in synthesis Nuclear pre-mRNA processing Lyon (IGFL) UK MRC Laboratory of Molecular Biology UK Wellcome Trust Centre for Cell Biology, Mads Gyrd-Hansen University of Edinburgh Ubiquitin signalling Hai-Kun Liu Michael Potente UK Ludwig Institute for Cancer Research, Central nervous system stem cells Angiogenesis and metabolism Thomas Wollert University of Oxford DE German Cancer Research Center (DKFZ) DE Max-Planck-Institute for Heart and Molecular mechanism of autophagy Lung Research DE Max-Planck-Institute of Biochemistry Mario Halic Massimiliano Mazzone small RNA mediated heterochromatin Macrophages in ischemia and cancer Halyna Shcherbata philip Zegerman formation BE Vesalius Research Center, VIB & KU Leuven miRNAs in cell differentiation and Regulation of genome replication DE University of Munich (LMU) maintenance UK Wellcome Trust / CRUK Gurdon Institute Yuki Nakamura DE Max-Planck-Institute for Biophysical Sebastian Hiller Lipid diversity in plant development Johannes Zuber Chemistry Outer membrane protein biogenesis TW Academia Sinica Cancer drug target identification with RNAi CH Biocentre, University of Basel AT Research Institute for Molecular Pathology (IMP)

Installation Grantees 2014 Nuno Barbosa-Morais Ana Domingos Günes Özhan piotr Setny Cancer transcriptomes and metastasis Neurobiological control of obesity Wnt b-catenin signalling hydration effects in proteins PT Institute of Molecular Medicine, Lisbon PT Gulbenkian Institute of Science, Oeiras TR Dokuz Eylul University, Izmir PL University of Warsaw Moving from: Moving from: Moving from: Moving from: CA University of Toronto US The Rockefeller University, New York DE Technical University Dresden DE Technical University Munich Tolga Çukur peter Lukavsky pavel Plevka Gerhard Wingender Investigation of the visual system Molecular basis of aberrant splicing structural studies of picornaviruses Invariant natural killer T cells in allergy TR Bilkent University, Ankara CZ CEITEC, Masaryk University, Brno CZ CEITEC, Masaryk University, Brno TR Bahçesehir University, Istanbul Moving from: Moving from: Moving from: Moving from: US University of California, Berkeley US Stanford University US Indiana University US La Jolla Institute for Allergy & Immunology

Events events.embo.org/science-society-conference Upcoming deadlines embo members EMBO Members Marie-France Carlier and Thomas EMBO Keynote Lectures Surrey are the organizers of the Jacques Monod 1 June Conference Actin and Microtubule Cytoskeletons in Cell Motility and Morphogenesis: an integrated view, to EMBO Young Investigators be held in Roscoff, France, from 26–30 May 2015. 1 April For full information visit http://sites.google.com/site/ EMBO Installation Grantees CJMac4nMT 15 April embo members The EMBO Meeting 2015: Registration is now open for the Meeting on the and Early registration and abstract Molecular Biology of Ageing in Groningen, the submission deadline: 10 June Netherlands, from 25–28 October. The meeting is co-organized by EMBO Member Ellen Nollen. The EMBL ATC, Heidelberg, Germany goal of this meeting is to bring together scientists working in the diverse research areas that are relevant for understanding the biology of aging. Paper submission and registration: www.bioageing.nl/ Editorial Next issue embo members EMBOencounters Register for the Applied Bioinformatics and Public Managing Editor E-Newsletter & Health Microbiology conference by 8 April: Barry Whyte Web version The next EMBOencounters issue – https://registration.hinxton.wellcome.ac.uk/display_ info.asp?id=474 Editor Yvonne Kaul Summer 2015 – will be dispatched in The meeting will be held from 6-8 May at the Yvonne Kaul July 2015. Wellcome Trust Genome Campus in Hinxton, Print & Web layout Cambridge, United Kingdom. Please send your suggestions, contributions Sandra Krahl and news to [email protected] by 15 May.

advancing the life sciences 2015 Birmingham United Kingdom 5 – 8 September

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