Opening up the Scientific Literature Meet the New EMBO Young

WINTER 2017

ISSUE 37

28 researchers selected Meet the new EMBO Young Investigators PAGES 4 – 5

Award for SourceData Open Access Opening up the scientific Going for gold for a literature sustainable future PAGE 3 PAGE 11

Transparency at EMBO Press Recognition of excellence Celebrating 10 years ERC Responsible and accountable publishing Newest EMBO Members welcomed Frank Gannon recounts how it came into being at annual meeting

PAGE 6 PAGE 7 PAGE 10

www.embo.org Table of contents

EMBO NEWS SCIENCE POLICY © Marietta Schupp, EMBL Photolab Marietta Schupp, ©

SourceData wins publishing Open Access: why green is not the new innovation award Page 3 gold Page 11 Editorial

Welcoming 28 new Young ith the announcement that all publicly funded research in Investigators Pages 4 – 5 WEurope must be freely accessible from 2020 onwards, the European EMBO Press brings more transparency Union firmly anchored Open Access in the to publishing Page 6 future of scientific publishing. It’s an ambitious target, and in the quest for solutions, we mustn’t overlook the need for publish- Women in Science Awards ing models that are sustainable in the long presented Page 6 term (p 11). SCIENCE STORY At the same time, the ‘when’ and ‘how’ to make scientific papers openly available Non-coding RNAs – where are not the only questions we must think about. Making an article available for free next? Pages 12 – 13 on the internet does not necessarily mean that interested readers, whether they are scientists or not, are able to find and bene- EMBO community fit from the publication. Back in 2009, the 50 millionth scientific Updates from across Europe article was published. With an estimated growth rate of between 8 and 9%, we will Pages 14 – 16 EMBO NEWS be approaching double that figure in the next two years. Adding to that the fact that the figures and data, which lie at the heart Newest EMBO Members meet in Awards and publications of a scientific publication, are not easy to Heidelberg Page 7 search, it is becoming increasingly difficult Achievements and papers by members to identify relevant work and keep up with EMBO at Basel Life: a snapshot Page 8 the latest studies in a field. of the EMBO community Page 17 EMBO’s SourceData platform offers a solution by turning figures into search- EMBO | EuropaBio Fellowships open able entities (p 3). By creating machine- for application Page 9 EMBO events readable descriptions of scientific figures, SourceData makes scientific data more Strengthening ties with the Taiwanese Upcoming courses, workshops and discoverable. A proof-of concept showed that the approach works. The next step will Ministry of Science and Technology conferences Page 17 be to work with the community to embed Page 9 SourceData more widely to make sure we really can open up the scientific literature. Frank Gannon reflects on the birth of Fresh from EMBO press the ERC Page 10 Some of our latest publications at a Maria Leptin Director, EMBO glance Page 19

n the biological sciences, most of the data Generating the metadata from figures that are supervision to ensure the quality of the informa- produced are published in the form of figures. necessary for SourceData’s capabilities means tion extracted, explains SourceData project lead IHowever, the search tools used to find identifying the biological entities – the proteins, Thomas Lemberger. “The important task of iden- published papers are usually limited to keyword- molecules or genes – referenced in each figure tifying discrete, named entities from text input based text searches. and legend, as well as their relationships. is one that can be addressed by automated text- EMBO’s SourceData platform generates a Eva Benito-Garagorri, who recently joined mining technologies.” description of these figures, and the data and SourceData as Scientific Coordinator, explains To explore how text-mining can be used as relationships they contain, in a machine-reada- further: “Interpreting this information is rela- part of the curation workflow, SourceData joined the 6th BioCreAtIvE (Critical Assessment of Information Extraction systems in Biology) challenge. As part of the challenge text-miners are SourceData wins ALPSP award invited to use the SourceData dataset to train and assess algorithms that match entities found in SourceData received recognition from the which brought together many of the major figure legends with their identifiers from stand- scientific publishing community when it was publishing houses. Both SourceData and Publons ardised biological taxonomies such as Uniprot or awarded the ALPSP Award for Innovation in (publons.com) received awards for innovation ChEBI, and then output the results in a suitable Publishing 2017. The annual award from the and were praised by the chair of judges, David format for SourceData. Association of Learned and Professional Society Sommer, who said: “Our winners are the result of Publishers (ALPSP) recognises outstanding inno- successful collaboration and partnership work- Opening new avenues with artificial intelligence vators in scholarly and professional publishing. ing within the industry to make a positive differ- The potential for automation in the SourceData SourceData was presented with the award on 15 ence to the academic community for the good of curation workflow does not end with entity recog- September 2017 at a ceremony in Amsterdam all.” nition. Thomas Lemberger explains: “We know that machine learning is making rapid progress in being able to extract meaning from natural language. Such methods are used by Twitter to identify sentiment, and by Google Translate to interpret the meaning of phrases. In our case, the task is to identify the nature of the relationship between entities – which one is influencing the other?” While this methodology remains in development, Lemberger is looking towards new para- digms whereby artificial intelligence algorithms improve themselves by learning from corrections made by expert curators and authors during publication. Successful implementation would make SourceData one of the first examples in publishing of coupling the expertise of scientists with the capabilities of machine learning models. This would open new avenues in scientific publishing, extending SourceData’s mission to the extraction and organization of structured Thomas Lemberger accepts the ALPSP award 2017. scientific knowledge. © The Association of Learned & Professional Society Publishers & Association of Learned The ©

More information: sourcedata.embo.org

ble format. As a result, articles can be searched tively easy for humans with the appropriate Liechti R, George N, Götz L, El-Gebali S, Chasapi A, based on the data shown in their figures, and scientific background, so figures are currently Crespo I, Xenarios I & Lemberger T (2017) SourceData figures that display related results can be linked processed for SourceData by professional bio- - a semantic platform for curating and searching across papers. The method for this has now been curators.” However, developments in machine figures, Nature Methods 14: 1021-1022. Doi: published in a paper authored by EMBO project learning could mean that the future holds a faster 10.1038/nmeth.4471

team members and their collaborators at the and easier way to extract the information from Editorial: The search for data, Nature Methods 14: Swiss Institute of Bioinformatics (Liechti et al., figure legends. 1017 Nature Methods, 2017). The SourceData approach has the potential Automation for faster curation to accelerate scientific discovery and “could The SourceData platform remains in active devel- fundamentally shift how scientists interact with opment with the goal of establishing an open and the collective body of knowledge and open up effective standard for the discovery and re-use of all data to synthesis, reassessment and reuse”, as scientific data. One of the next steps in develop- highlighted in a recent editorial (Nature Methods, ing the platform is the acceleration of the figure November 2017). curation workflow while keeping expert-based

Welcoming the new EMBO Young Investigators 28 group leaders from 11 countries join the

EMBO community Filipe Cabreiro Bacteria: macromolecular machines for nutrition and 28 young researchers were elected drugs as EMBO Young Investigators London, GB this year. They join a network of 47 current and 417 past Young Investigators who represent some of the best up-and-coming group leaders in the life sciences in Europe and beyond.

“It is a pleasure to welcome these Axel Innis Nicola Iovino Manuel Irimia Ribosome inhibition Epigenetic regulation of Transcriptomics of outstanding scientists to the by nascent or fertilization vertebrate development antimicrobial peptides Freiburg, DE and evolution EMBO community,” says EMBO Bordeaux, FR Barcelona, ES Director Maria Leptin. “Between them, they carry out some very promising life science research that Europe has to offer, and we look forward to supporting them in their professional and scientific endeavours.” Daniel Messerschmidt Patrick Müller Elizabeth Murchison Epigenetic reprogramming Quantitative analysis, Genetics and evolution The new Young Investigators are and its implications in control,and engineering of of transmissible cancers based in 11 different countries, development and disease embryonic signalling systems in dogs and Tasmanian Singapore, SG Tübingen, DE devils including European Molecular Cambridge, GB Biology Conference (EMBC) Associate Member States India and Singapore.

Selection to the EMBO Young Investigator Programme is © Bruederli © recognition of exceptional research Magdalini Polymenidou Alvaro Rada-Iglesias Guadalupe Sabio and scientific potential. Through Molecular pathogenesis of Transcriptional regulation in p38MAPK signalling neurodegenerative diseases development and congenital pathway the programme, EMBO identifies Zurich, CH disease Madrid, ES Cologne, DE and supports researchers under 40 years of age who are in the process of establishing their own laboratory. In addition to financial support, they receive a range of benefits for themselves and their groups (see box).

Noam Stern-Ginossar Joanna Sulkowska Dario Riccardo Molecular networks of SPOUT methyltransferase Valenzano viral-host interaction enzymes Evolutionary and Rehovot, IL Warsaw, PL experimental biology of ageing Cologne, DE

Jeffrey Chao Luisa Cochella Katie Doores Luca Giorgetti Imaging mRNAs in single Transcriptional and post- Glycosylation in infectious Mechanisms of long- cells transcriptional origins of diseases range transcriptional Basel, CH cellular diversity London, GB regulation Vienna, AT Basel, CH

The programme at a glance During their three-year tenure, © Schmelz-Fotodesign ©

Sonja Lorenz Dahai Luo Joao Matos EMBO Young Investigators Structural mechanisms of Mechanisms of viral Mechanisms of receive a range of benefits: ubiquitin signaling infection and host defense genome stability and Wuerzburg, DE Singapore, SG haploidization Zurich, CH Support for Young Investigators ➔➔ 15,000 euros award ➔➔ Up to 10,000 euros additional funding ➔➔ Childcare support ➔➔ EMBO Research Leadership course

Support for their labs ➔➔ Young Investigator PhD course and local courses ➔➔ Meeting grants and Nobel laureate Vladimir Pena Hendrik Poeck Sophie Polo meeting Structural basis of splicing Cytosolic nucleic acid sensors Epigenome maintenance in regulation and DNA-based in tissue homeostasis and response to DNA damage ➔➔ Visits to other labs catalysis cancer immunotherapy Paris, FR GÖttingen, DE Munich, DE ➔➔ Access to EMBL core facilities ➔➔ Lab retreat and creativity facilitation ➔➔ Listing of job vacancies

Networking opportunities ➔➔ Annual Young Investigator meeting ➔➔ Sectoral meetings ➔➔ Institute visits ➔➔ Support for European networks of junior PIs Schraga Schwartz Elena Seiradake Arun Shukla Cracking the Adhesion G protein-coupled Structure, function and ➔➔ Joint group meetings epitranscriptome receptor complexes allosteric modulation of G Rehovot, IL Oxford, GB protein-coupled receptors Kanpur, IN Helping them get noticed ➔➔ Lecture grants ➔➔ Conference support for organisers ➔➔ Listing of awards and publications in print and on social media ➔➔ Inclusion in the EMBO directory and an online database ➔➔ EMBO Press publishing fees covered

More information: Louis Vermeulen Yue Wan Colon cancer heterogeneity RNA structure and genomics embo.org/funding-awards/ Amsterdam, NL Singapore, SG young-investigators

Responsible and accountable publishing EMBO Press brings more transparency to the publishing process

upporting researchers and stimulating the “At EMBO Press, we want you to trust in the “For us, transparency extends beyond peer exchange of scientific information are two quality of our editorial process and the research review,” adds Pulverer. “To encourage open data Sof EMBO’s core goals. This is why EMBO we publish. We have confidence in the proce- sharing, we invite authors to publish their source Press offers authors a fair and transparent dures of our journals, so we aim to be as transpar- data – the minimally-processed experimen- publishing process. ent as possible, from start to finish,” says Head of tal results underlying their figures.” Scientists All four EMBO publications, The EMBO Journal, Scientific Publications, Bernd Pulverer. can also publish replicates, structured datasets, EMBO Reports, EMBO Molecular Medicine and In addition, the editors will respect an author’s models and detailed protocols to support the key Molecular Systems Biology, employ transparent choice to exclude specific referees from peer claims in their paper. peer review. Authors can choose to publish the review. And there are no confidential reviewer referee reports, editorial correspondence and comments, meaning authors and readers can see embopress.org/a-different-way-to-publish decision letters alongside their paper, and more exactly what EMBO Press editors use to make than 95% of authors do. their decisions.

Honouring two outstanding scientists Ottoline Leyser and Fiona Watt receive their FEBS | EMBO Women in Science Awards

he recipients of the 2016 and 2017 FEBS | EMBO Women in Science Awards received Ttheir prizes during this year’s FEBS Congress, which took place in Jerusalem, Israel, between 10 and 14 September 2017. Fiona Watt and Ottoline Leyser each delivered an award lecture on their work as part of the conference programme. Ottoline Leyser (centre) receives the Women in Science Award certificate and statuette from Hermona Fiona Watt, who is the Director of the Centre

Soreq (left) and Cecilia Arraiano, Chair of the FEBS Women in Science Working Group (right). Hanni Naor © for Stem Cells and Regenerative Medicine at King's College London, UK, received the award in 2016 for uncovering the mechanisms that control Sainsbury Laboratory at Cambridge University, challenges that women face when pursuing a mammalian epidermal stem cell renewal and UK, for her work on the evolutionary, develop- career in science and for acting as strong mentors differentiation, and for discovering how these mental and biochemical mechanisms that enable for the next generation of scientists. Fiona Watt processes are deregulated in cancer, wound heal- plants to respond and adapt to environmental said on accepting the award that “science would ing and inflammatory skin disorders. changes. be better if it were all inclusive, and that a great This year’s FEBS | EMBO Women in Science Both scientists were also recognized for deal still remains to be done to champion and © Hanni Naor © Award went to Ottoline Leyser, Director of the their commitment to exposing the barriers and embed diversity.”

Recognition of excellence EMBO welcomes its newest members to the organisation

s a student and postdoc, reading about reception at the EMBO building offered members feedback or insight on topics relating to EMBO scientists being elected as EMBO an opportunity to meet each other as well as activities, EMBO Members are an integral part of “A Members was something that felt miles EMBO employees in an informal setting. the organization. away, something that would happen to excellent, Roberto Sitia from the Vita-Salute San Raffaele For Sitia, who served on the Courses and ‘grown-up’ scientists,” says Renata Basto from the University, Milan, Italy, who was elected as an Science & Society Committees in the past, partici- Institut Curie in Paris, France, about being elected EMBO Member in 1992 and has attended several pation in EMBO activities has two main advan- to the EMBO Membership this year. of these meetings, particularly values the oppor- tages. He explains: “You are part of an equilib- “Being elected feels almost like passing the tunity to meet researchers from other disciplines. rium: you give back some of what you are given finish line – like an acknowledgement that I am not a junior scientist anymore,” she continues. “But it is not only about recognition by my peers. Who are the EMBO Members? It is also about recognition of the originality of the work that we, as a lab, have been developing. ➔➔ In total, 2183 scientists have been elected to the EMBO Membership since its foundation And that is highly motivating.” in 1964. Membership is lifelong. Today, just over 1700 scientists make up the EMBO The EMBO Membership encompasses more Membership. than 1700 of the best life scientists in Europe ➔➔ EMBO Members and Associate Members live and work in 41 countries around the world. and around the world. Members and associ- ➔➔ Women make up 18% of the EMBO Membership (an increase of 3% since 2010). ate members are elected on the basis of their outstanding achievements in the life sciences. ➔➔ The average age of newly elected members in 2017 was 50.8 years. “I was pleased to welcome an additional 65 ➔➔ Members represent all areas of the life sciences. Molecular medicine, signal transduction and great scientists to our organisation this year,” development are the most highly represented subject areas. says EMBO Director Maria Leptin. “We received more nominations than ever before during this An online directory with all EMBO Members is available at http://people.embo.org/ election cycle, which pays tribute to the strength and diversity of the European life sciences.” He explains: “the trend of modern science often in return. And you get to meet interesting people Connecting with each other forces people to follow their own discipline in and receive different views.” In order to celebrate their election, each year depth, and sometimes one forgets to regard and Newly elected EMBO Member Panayiota EMBO invites all new members to a formal meet- enjoy the work of ‘research neighbours’.” Poirazi from the IMBB-FORTH, Heraklion, Greece ing in Heidelberg, which also offers an opportu- adds: “As an EMBO Young Investigator, I already nity to find out more about the organization. An integral part of EMBO benefited from many of the organization’s activi- This year’s meeting took place between 18 The participants at the Members’ Meeting also ties. Therefore, I sincerely appreciate the effort and 20 October 2017. 58 new members elected in heard from EMBO Director Maria Leptin and and commitment required by EMBO Members to the last few years were joined in Heidelberg by 19 EMBO Head of Scientific Publications Bernd maintain the organization’s very high standards of their nominators (namely, previously elected Pulverer about the ongoing activities and some and expand to new horizons. That’s why I’m members) for three days of presentations and of the latest initiatives at EMBO and EMBO Press. eager to help towards this challenging goal.” discussions. Each of the new members present- Whether it is through formal roles on Council or a ed their research in a short talk. A welcome committee, or more informally, through providing

Impressions from EMBO at Basel Life. Sir Paul Nurse (top right) and Jennifer Doudna (bottom right) gave presentations. Paul Nurse with EMBO Member and next year's keynote speaker Michael Hall (middle right).

EMBO at Basel Life New conference connected scientists in academia, industry and the clinic

he EMBO at Basel Life conference is the discussed work on all aspects of genome biology, work on exploring the origins of modern humans newest kid on the block in European life ranging from microbial genomes and genome through sequencing ancient genomes. Tscience meetings. The conference was evolution to transcription, inheritance and clini- With the Louis-Jeantet Prize lectures the conceived as broad-scope scientific event on cal approaches as well as techniques, including conference celebrated the achievements of the current and emerging life science research. Its single molecule imaging and bioinformatics. 2017 prize winners: neurobiologist Silvia Arber first installment took place form 10-13 September The meeting kicked off with a public lecture and immunologist Caetano Reis e Sousa. The two 2017 in Basel, Switzerland as part of Basel Life, an titled “What is life?” by Nobel laureate and EMBO scientists presented their research on movement- initiative organised by researchers from academ- Secretary General Sir Paul Nurse. He described controlling neuronal circuits and the mechanisms ia, pharmaceutical and biotechnology industry the fundamental features of life while draw- for sensing pathogen invasion and tissue damage, and the City of Basel. ing attention to paintings, which convey these respectively. “The conference fostered the exchange between features and which are exhibited at the Basel Art The second EMBO at Basel Life conference researchers from academia, clinics, and industry, Museum, where he gave his talk. will take place from 11-14 September 2018. and promoted excellence in the life sciences,” said Jennifer Doudna, co-discoverer of the CRISPR- EMBO Member and scientific co-organizer Susan Cas9 technology, discussed genome engineering www.basellife.org/embo Gasser from the Friedrich Miescher Institute for research as well as the possibilities and challeng- Biomedical Research in Basel. More than 600 es resulting from it in her keynote lecture. Svante established and young researchers presented and Pääbo, the second keynote lecturer, presented his

Four six-month fellowships for bioinformatic analyses of WGS using patient- The goal of the EMBO | EuropaBio Fellowships research exchanges available parent trio data, and I was able to identify candi- is to facilitate collaborations with research date pathogenic variants in five genes not previ- groups applying techniques that are unavailable ulika Sumathipala is a PhD student at the ously associated with disease.” in the applicant's laboratory. EuropaBio, which University of Oslo, Norway. Her research represents 79 corporate and associate members Dexplores the pathogenicity of non-coding Funding for 2018 visits and bio-regions, and 17 national biotechnology variants in whole genome sequencing (WGS) To support research exchanges in the areas of associations, provided funds for these addition- data in children with severe neurological disor- systems biology, genomics & computational al fellowships as part of the collaboration with ders. To advance her research, Dulika applied for biology, EMBO is funding up to four additional EMBO. an EMBO Short-Term Fellowship, which enabled fellowships in 2018. These EMBO | EuropaBio The application deadline for EMBO | EuropaBio her to spend some time in Christian Gilissen’s Fellowships are being offered in partnership Fellowships is 31 December 2017, and applicants group at Radboud University Medical Center in with the European Association for Bioindustries should plan their visits to take place in 2018. Nijmegen, The Netherlands. (EuropaBio). Compared with regular EMBO Explaining how this time in another laboratory Short-Term Fellowships, researchers can apply embo.org/funding-awards/fellowships/ helped her, she says: “During the stay I learnt for extended laboratory visits up to six months. embo-europabio-fellowships

EMBO delegation visits Taiwan Series of events marks 5th anniversary of cooperation agreement with the Ministry of Science and Technology

n November 2017, a delegation from EMBO travelled to Taiwan to celebrate the existing Ipartnership with the Ministry of Science and Technology (MOST) and to intensify interactions with the Taiwanese scientific community. MOST and Academia Sinica signed a cooperation agreement with EMBO five years ago, which allows life scientists based in Taiwan to benefit from a range of EMBO activities. EMBO Member Bertrand Jordan, who headed the delegation, explains: "The trip was organized to mark the 5th anniversary of this agreement and the ongoing commitment to continue and develop this cooperation.” The visit included several days of presentations, meetings and group discussions, which began with a scientific symposium at the Academia Sinica. In addition to learning from EMBO repre- sentatives about EMBO funding, training opportunities and science policy work, the participants also heard scientific presentations from EMBO Members, EMBO Young Investigators and other Head of Scientific Publications, Bernd Pulverer, talks about EMBO Press. life scientists in Taiwan. During the following days, the EMBO delegation visited National Yang-Ming University and visit strengthened the interactions with the EMBO Furthermore, Michele Garfinkel and Sandra National Taiwan University. The EMBO repre- community and provided the opportunity for us Bendiscioli delivered an EMBO workshop on sentatives spent a day at each university, where to present our scientific achievements from the Research Integrity at the Academia Sinica. The they presented EMBO’s activities to an audience partnership. We look forward to extending the day-long interactive workshop included presenta- ranging from students to faculty members. cooperation with EMBO so that the partnership tions and discussions on the value of responsible Bertrand Jordan adds: “One of [the visit’s] can catalyze more scientific interactions.” research conduct, the nature of scientific miscon- most successful features was the contact with Throughout the events, Head of Global duct, conflicts of interest, publication issues, many younger scientists, including students, that Activities Luis Valente, Head of Scientific mentoring and good data practice. allowed extensive discussions and raised aware- Publications Bernd Pulverer, Science Policy ness of the possibilities offered by EMBO. I fully Programme Manager Michele Garfinkel and embo.org/about-embo/global-activities expect this will lead to a surge in the number Science Policy Programme Officer Sandra of activities connecting Taiwan with EMBO and Bendiscioli met with researchers in small groups European science." or individually to discuss how EMBO supports Woei-Jer Chuang, Director General of the scientists and how those based in Taiwan can Department of Life Science at MOST says: “This benefit from the activities that EMBO offers.

©2017 EMBO EMBOencounters | Winter 2017 | [email protected] 9 SCIENCE POLICY The ERC: from before then to anniversary celebrations Former EMBO Director Frank Gannon shares the story behind a series of meetings that propelled the European Research Council from idea to reality.

he European Research Council (ERC) is ten from scientists. Together with EMBL we formed years old. This beautiful child has thrived the European Life Sciences Forum (ELSF). It Tand its many parents should look at it started with an open meeting at UNESCO in with pride. At the turn of the millennium, many Paris in 2003 to represent voices from the scien- ©Tony Phillips scientists had given up hope that such a struc- tific community. The meeting quickly galvanised ture could come into being. That view turned out around the concept of an ERC to support excellent to be wrong, because of an unusual persistence basic research. Most of the 300 scientists present Frank Gannon by scientists and the organisations that repre- strongly expressed the opinion that “their” ERC sent them, and a change in the rhetoric of the should be at arm’s length from the EC, because European Commission (EC). Ever since, the EU they did not trust the EC’s selection processes or And so we are celebrating ten years of the has nurtured and supported the council, which the concept of juste retour, by which countries ERC. The scientific community has engaged with it now rightfully presents as one of its major tended to gain as much in grants as they contrib- enthusiasm, as the spirit of the ERC is clearly in successes. uted to the Framework Programme. In addition, line with the ideas of those who participated in the requirement that research must have an its formation: to identify and support excellence. From idea to formal consideration economic impact was contrary to the focus on The idea of an EU funding agency for basic basic research. Busquin attended the meeting Developing for the long haul research moved from the agenda of scientists to and expressed his enthusiasm for an ERC, but However, there is some reason for concern as that of decision makers at a meeting to discuss stressed the technical and political problems. some countries have such a low level of success future EU expenditures in Sweden in 2001. At The ELSF, soon joined by other organisations, that it must be demoralising for their research- that time, the Danish government held the EU continued to hold meetings that refined what the ers and for their politicians. To illustrate the Presidency and the Commissioner for Research, ERC should be. Questions arose at an early stage problem: with a budget of 1.67 billion euros in Phillipe Busquin, was using the idea of a as to restricting it to the life sciences as a pilot 2016, the ERC awarded eight grants to Poland, European Research Area (ERA) to obtain more project, whether support of research infrastruc- the Czech Republic, Estonia and Portugal collec- funding for research in the 6th EU Framework ture should be included, and how to encourage tively, whereas 34 grants went to the Netherlands, Programme. interdisciplinary projects. Some of these (espe- which was the fourth ranked country. And At the Stockholm meeting, economists argued cially how to support interdisciplinary research) University College London alone accounts for that the EU Agricultural Policy, which garnered remain pertinent and unresolved until today. At many more grants than all Eastern European 50% of EU spending, was merely an excessive each of these meetings, the EC sent a high-rank- countries combined since the start of the ERC. subsidy and that the money would be better spent ing official, and their messages were encouraging In my view it would be good for European on research. However, the legal basis of the EU’s but always came with new pre-requisites. science and for the long-term success of the ERC, Framework Programme only allowed it to support Because of the strength and cohesion of its if there were a second-tier competition. Such a research with potential economic benefits. Many organisations, the life sciences were spearhead- special excellence-based funding restricted to also questioned the value of basic research per ing these discussions, but soon recognised that competitive researchers in countries that are in se. Nonetheless, the concept of an ERC was up this could seem like special pleading. In 2004, the lower half of the success league could stimu- for discussion, and even at that 2001 meeting the ELSF broadened its base to include all natural late better research throughout Europe and help funds for it were placed in the billion euros brack- sciences, social sciences and the humanities and retain the best scientists in the countries that et. Where would that money come from? There established the Initiative for Science in Europe most need them. It could also avert a possible were two responses: either from the EU, or from (ISE). Now the barricades were manned by backlash against the ERC by those member states national research funding agencies. It left many scientists from all disciplines who repeated the that are getting fewer awards. wondering if anything would happen next. message: “What do we want? ERC! When do we Now, the ERC heads into its teen years. These Luckily, the Danes had already planned ahead want it? Now!” could be turbulent – for instance, the potential and organised a meeting in Copenhagen in 2002 impact of Brexit – but it is also the time for matur- called “Towards ERA: Do we need a European Re-interpreting the law ing and decisions for the longer haul. And yet, Research Council?” By the end of the meet- But an impasse had been reached around the there is plenty to celebrate. The ERC has provided ing, the answer was a resounding “Yes”. The question of who would fund the ERC. Then, in scientists with the opportunity to explore inter- Danish government, working with Julio Celis, a complete volte face, Achilles Mitsos, the EC’s esting new ideas and to be daring. All involved who was Secretary General of the Federation of Director General for Research, gave a speech since its launch – the ERC Scientific Council, the Biochemical Societies (FEBS) and the Danish at an ISE-organised meeting in 2005 where he Steering Committee, the EC, and the hundreds of EMBC representative, then established a working re-interpreted the EU laws: EU-wide competi- scientists – have done a great service to Europe. party under Federico Mayor, who had been the tion, including basic research, met the necessary As a proud parent I salute the ERC and the Director General of UNESCO. They prepared a pre-condition of “added value” for the member hundreds of other parents. Cheers! report for the EC, thereby making the ERC a topic states. The way was open to include the ERC in to be considered formally. the next Framework Programme in 2006. Clever This is an abridged version of an article first word-smithing (“basic research” became “fron- published in EMBO Reports (Doi: 10.15252/ Speaking for science tier research”) and fresh interpretations of trea- embr.201745025). While the machine of the EU turned at its own ties and rules were required, but once the EC had pace, FEBS and EMBO (in practical terms: Julio embraced the project, it moved forward very fast. and I) thought the process needed more input

Going for gold If we want to make Open Access sustainable and useful in the long run, we must choose ‘gold’ over ‘green’, argues EMBO Director Maria Leptin.

hen – back in May 2016 – the European can find alternatives, for example through charg- OA refers to journals that offer the choice to Commission announced its ambitious ing article processing charges (APCs), although publish OA). But if we want to ensure a success- Wtarget of making all publicly funded these may not cover all the costs for running a ful OA future, our community, including authors, research in Europe openly accessible, it joined a highly selective journal. funders, publishers and policymakers, must take host of countries, funders and research organiza- In the case of green OA, journals remain stock and develop a coordinated effort that maxi- tions pushing for change in scientific publishing. responsible for publishing the final peer-reviewed mizes the advantages of OA and makes it a viable The Registry of Open Access Repository and revised version of a paper, but face subscrip- option for the long term. Mandates and Policies (ROARMAP) currently tion losses because a version of the paper can be To enable a complete move to OA, we need includes more than 880 open access mandates freely accessed elsewhere. to find a sustainable and fair way to pay for and policies worldwide. That is double the There are other disadvantages of green OA, too. the services that are provided by journals. Even number registered only five years ago. But Not all institutional repositories are well indexed with a financial model that does not include any despite a growing desire for Open Access (OA) or well connected, or have a guaranteed long- profit, providing a quality publishing service still publishing, a viable option for making scientific term source of secure financing, meaning the costs a lot of money. Of the currently available output freely available in a way that is structured, papers are less discoverable than those published models, only gold OA offers the potential for such curated, and quality-controlled as well as finan- in journals. The running of multiple repositories a solution. As it stands, services like peer review, cially sustainable still seems some way off. holding duplicate files also results in additional quality control and archiving are associated with costs. Further, some publishers don’t allow post- publishers, but there is no reason to say that that From sound idea to confusing reality ing of the final, reviewed and edited manuscript, will always have to be the case. These services Growing out of the initial desire of individuals which has implications for the scientific record. should be carried out by professionals, and must to make scientific findings more widely acces- The posting of earlier manuscript versions in an be adequately financed, no matter what type of sible, the OA movement has resulted in numer- institutional repository has two important conse- organization these professionals are associated ous initiatives from publishers, funding bodies quences: if the versions are not clearly linked, it with. and individual researchers. And while every- one is, in principle, aiming for the same thing, namely to ensure that the outputs of scientific work are not hidden behind paywalls, the many Open Access Week 2017 different mandates, policies and recommenda- tions on what OA should be and how it should Between 23 and 29 October, scientists, journals, libraries, institutes and organizations across the be financed mean that there is now a danger of world took part in Open Access Week 2017. Under the theme “Open in order to…”, discussions, work- diverging from this initial aim. shops and events focused on all aspects of open access. Head of Scientific Publications at EMBO, Bernd One example of this is green OA, which is an Pulverer, took part in an event organized by the European Molecular Biology Laboratory (EMBL) Szilard expensive halfway house with limited benefit to library. Pulverer said: “Open Access is an important driver to ensure broad access to the scientific litera- the scientific community or indeed the public. ture. But we must not drive down costs so much as to erode the quality control function of the publish- ‘Green’ describes the archiving of a version of a ing process. If framed correctly, Open Access will preserve quality assurance, while also allowing the published paper in public repositories or on serv- sharing, archiving and discovery of all significant research outputs.” ers hosted by researchers’ institutions. Here, it is freely accessible, usually after a certain embargo period stipulated by the publisher. By contrast, the ‘gold’ OA model means that the journal in can easily lead to confusion over what the copy Thinking beyond the models currently in place, which a paper was published grants immedi- of record is, and it denies readers access to the it is, of course, possible to envisage entirely differ- ate free access to the final version of the article. improvements and data added through the peer ent solutions that revolutionize the reporting and Green OA might look appealing at first, but if we review, editing, curation and quality control archiving of scientific findings in the long term. want OA to work in a sustainable manner for processes. Finally, green OA means that either For now we must accept that creating a scientific papers in high-quality, peer-reviewed journals, it authors themselves or their institutions become literature that is not only openly accessible but has to be gold, not green. responsible for the posting of corrections or also reliable comes at a cost, and a fair way of retractions to make sure readers using the green financing that service will have to be found. Why is green OA unsustainable? OA repositories are aware of them. In the traditional, subscription-based model, scientific publishers cover the cost for the servic- Finding a sustainable model es they provide through subscriptions. In the For some time now, green, gold and hybrid OA case of gold OA, the income from subscriptions publishing models have been developing side by is removed because libraries and individuals no side in addition to initiatives on preprint post- longer need to pay to access papers. But journals ing, open databases and repositories (hybrid

Small RNAs play a crucial role during Salmonella infections. Salmonella (green) infecting HeLa cells (nuclei are shown in blue, mitochondria in red). © Alexander Westermann ©

The non-coding genome Non-coding RNAs make up huge regulatory networks that tune cellular processes. The organisers of the recent EMBO | EMBL Symposium on the topic discuss the emergence of the field and where it is going.

By Katrin Weigmann

he real voyage of discovery consists not brought together scientists working on all aspects between about 6–20 base pairs. In particu- in seeking new landscapes, but in having of non-coding RNAs. lar, microRNAs in most animal cells primar- “Tnew eyes,” wrote French author Marcel ily use a short seed sequence of six nucleotides. Proust in his novel Remembrance of Things Past. Ubiquitous regulators Accordingly, they each have many targets – about And while Proust was, in fact, describing art, he There are thousands of different non-coding 400 on average and provide a whole additional might just as well have been referring to science. RNAs in each cell. But while they are numerous, layer of regulation that affects almost every Often, innovative technologies provide research- their mode of action is usually subtle, and this process in the cell. ers with ‘new eyes’ to look deeper into well-stud- could be, according to Vogel, the other reason ied matters. they have been overlooked for so long. “They Tuning a complex system High-throughput sequencing played a central often lack the strong phenotypes that we see The ability of non-coding RNAs to subtly down- role in understanding the richness of the non- when we knock out, for example, a transcription regulate the expression of multiple genes at once coding RNA world. “Until recently, we did not factor,” he explains. “The way they regulate gene makes them particularly well suited for fine- have the methodology to investigate these expression is very different, they are involved in tuning regulatory transitions. For example, in a molecules,” says EMBO Member Jörg Vogel of fine-tuning.” recent study Vogel showed that small RNAs play the University of Würzburg, Germany. But now The molecular mechanisms for many of the a crucial role during Salmonella infections, help- researchers are uncovering large regulatory small non-coding RNAs of plants and animals ing the pathogen transit from an invasive state to networks consisting of non-coding RNAs that had is very similar: They associate with a protein a state of intracellular replication. “These sRNAs hitherto escaped detection. of the Argonaute family to form a silencing modulate response curves through feedback or This network of sRNAs, microRNAs, siRNAs, complex, and guide it towards a target mRNA. feed-forward loops. They can induce threshold piRNAs, lncRNAs and more was the focus of “It is a two-component system where Argonaute values for switching on genes or allow genes to the EMBO | EMBL Symposium “The non-coding provides the molecular function, and the non- be switched off more quickly. Depending on how genome” that took place in Heidelberg from coding RNA is responsible for target specific- the feedback loops are constructed, you will get 13–16 September 2017. The conference, which ity,” says David Bartel of the Massachusetts different time curves of gene expression,” says was co-organized by Jörg Vogel, EMBO Member Institute of Technology, USA. Moreover, base Vogel. Elisa Izaurralde, David Bartel and John Rinn, pairing with the target sequence is usually short,

Open questions remain Much has been learned about non-coding RNAs in the past decade, but there is more to be under- stood about their exact function, their target genes and their networks. “We do by now have a pretty good idea of how microRNAs work, but other classes have proven to be more challenging,” says Elisa Izaurralde of the Max Planck Institute for Developmental Biology in Tübingen. “piRNAs, for example, have been more difficult to understand and many mechanistic questions remain open. There may be more than one mechanism by which they regulate genes.” “For some of the RNA classes, an important future challenge will be to separate the signal from noise. Not everything that is transcribed will also have a function,” says Vogel. In addition, the diversity of non-coding RNAs is far from under- Meet-the-Speaker sessions offered participants stood. “Research thus far has concentrated on a an opportunity for in-depth discussions. few model organisms.”

“Start to learn the language” this approach to identify sequences and struc- The greatest challenge, however, is to understand tures required for nuclear localization of non- long non-coding RNAs (lncRNAs). There are coding RNAs. “The key is to have a functional many thousands of them and they are part of a assay,” he adds. “Once you have that you can very heterogeneous group, unified only by two start to learn the language”.

features as their name suggests – they are long EMBL Photolab Hugo Neves, © © Alexander Westermann © and non-coding. “It took about 10 years to do a Towards clinical applications cartography and to find out which RNAs to study. For decades, researchers have been using non- Now we are ready to investigate how they work,” coding RNA as a research tool to silence genes in says John Rinn from the BioFrontiers Institute a technology called RNAi. Today, this approach in Boulder, USA. According to Rinn, an impor- is also being used therapeutically. Although tant next step – admittedly, a very large one – is the start was slow – there are major problems to understand what he calls the syntax of non- in drug delivery and toxicity – there has been coding RNAs – the link between structure and some success. Only recently, pharmaceutical function. “We have a lexicon for the language of companies Alnylam and Sanofi announced posi- proteins, we understand words like ‘Zinc-finger tive phase 3 clinical data for their RNAi-based domain’ or ‘kinase domain’. We can predict what drug patisiran that targets a rare genetic disease they are doing. The RNA language, in contrast, is known as hereditary ATTR amyloidosis with EMBO Member and conference still hieroglyphic to us. A big task for the future polyneuropathy. co-organiser Jörg Vogel. will be to translate these hieroglyphs into mean- Aside from treating human cells with RNAi, ing,” says Rinn. Jörg Vogel sees another option in targeting bacte- High-throughput technologies will play a ria. The advantage of RNAi over classic antibiot- our goals is to specifically manipulate or elimi- major role in this endeavor. “We can play with ics is that RNAi can act in a more refined way. nate some bacteria of the microbiome,” says the sequence through an evolutionary approach This is a great advantage when it comes to treat- Vogel. and change it a little and then see if it is still func- ing dysbiosis, a microbial imbalance that most tions,” says Rinn. He and colleagues have used often affects a person's digestive tract. “One of www.embo-embl-symposia.org/

An insider’s view

Coming from a background of bacterial genetics, Elisa Izaurralde (Max Planck Institute for of ours, it may be the act of transcription that The organisers of the EMBO | EMBL Symposium Developmental Biology): “Technological advances matters, because it induces chromatin remodel- “The Non-Coding Genome” talk about some of the now allow us to better understand the function of ling. While the RNA is being transcribed, it might most exciting questions and developments they RNA binding proteins. We can knock out proteins serve as a beacon to show proteins where to bind.” are investigating. such as argonaute using the CRISPR-Cas9 system Jörg Vogel (University of Würzburg): “Single David Bartel (Massachusetts Institute of and look at its effects using high-throughput cell RNA sequencing is becoming a very impor- Technology): “We are looking at a regulatory sequencing. Much work has thus far been done in tant topic. Gene expression can vary considerably network involving two microRNAs, one circular cell lines, it will be important to investigate func- between cells and this heterogeneity matters in RNA and one long non-coding RNA, that seem to tions at the level of the organism.” immune reactions and infection processes. There be regulating neuronal activity in the brains of John Rinn (BioFrontiers Institute): “Many non- are host cells that are more susceptible to infection mice. These studies involve genetic approaches, coding RNAs are transcribed at very low abun- and there are pathogens that are more aggressive which are easier to do now that we can more dance in a cell-specific manner, and the ques- than the larger part of the population. We are only quickly knock out each of the components.” tion is what they do. According to a recent model now starting to understand why that is.”

Giulio Superti-Furga, Erika Tuppy, Hans Tuppy, Maria Leptin, Anton Zeilinger (President of the Austrian Chemistry Academy of Sciences in Vienna), Heinz Faßmann (University of Vienna) Nobel Prize Tuppy Lectures honour one of for two EMBO EMBO’s earliest members Members

ans Tuppy is one of EMBO’s earliest at the Austrian Academy of Sciences in Vienna. MBO Members Jacques Dubochet members and an influential figure in Following an introduction by EMBO Member from the University of Lausanne, HAustrian science. In order to honour the Giulio Superti-Furga, Research Center for ESwitzerland, and Richard Henderson Austrian biochemist and his achievements, the Molecular Medicine in Vienna, she spoke about from the MRC Laboratory of Molecular University of Vienna and the Austrian Academy the interplay between the molecular processes Biology in Cambridge, UK, were awarded of Sciences initiated the Hans Tuppy Lecture within and between cells during morphogenesis. the 2017 Nobel Prize in Chemistry. series in 2016. The lectures are given by outstand- The previous two lectures in 2016 were Together with Joachim Frank from ing scientists who have made pioneering contri- presented by EMBO Members Kim Nasmyth, the Columbia University, New York, USA, butions to biochemistry or molecular biology. University of Oxford, and Sir Adrian Bird, Dubochet and Henderson received the On 29 June 2017, EMBO Director Maria University of Edinburgh. prize for the development of cryo-elec- Leptin presented the 3rd Hans Tuppy Lecture tron microscopy (cryo-EM) to determine high-resolution, atomic-level structures of biological molecules in solution. In the 1980s, Jacques Dubochet devised a way to vitrify water through rapid cool- ing – an approach that made it possible to Structural Genomics Consortium study biological samples under the electron micrograph. In 1990, Richard Henderson expands to Frankfurt and his colleagues showed the potential of using cryo-EM for biological imaging when he Structural Genomics Consortium (SGC) by developing highly specific chemical inhibitors they generated a three-dimensional, atom- is a public-private partnership that aims to called probes. ic level image of bacteriorhodopsin. Tfacilitate the discovery of new medicines by The scientists in Frankfurt will take the lead Dubochet and Henderson join 85 other ensuring free access to a wealth of research data in the new “pharma donated chemical probe EMBO Members and Associate Members and reagents. The enterprise is funded by non- programme”. Pharma companies hold numerous who were awarded Nobel Prizes. profit organizations and pharmaceutical compa- high-quality chemical probes against a wide array A free collection of recent research nies and includes six laboratories at academic of therapeutic targets. The majority of companies published in EMBO Press journals by institutions worldwide. Goethe University within SGC has now agreed to donate 70 such Joachim Frank and other scientists using Frankfurt recently became the first German site of hidden probes (along with broad characteriza- cryo-EM to unravel the beauty of biomol- the initiative. EMBO Members Volker Dötsch and tion data and relevant negative controls) to the ecules is available on the EMBO Press Ivan Dikic are actively involved in this endeavour, scientific community. These will be additionally website. which is led by Stefan Knapp. complemented by SGC labs and academic part- Scientists involved in the SGC have already ners, which include the NIH. www.embopress.org/cryo-em deposited more than 2000 high-resolution struc- www.embo.org/members/nobel-laureates tures of medically relevant proteins in public www.thesgc.org/ databases, and identified potential new targets

he Annual Meeting of the New Champions (AMNC) is held annually in ©World Economic Forum Benedikt von Loebell TDalian or Tianjin, China. As the World Economic Forum's global meeting on innovation, science and technology, it brings together business leaders, policymakers and scientists for discussions that are aimed at driving future advancements for the benefit of global society. EMBO Member Maria Elena Torres-Padilla from the Institute of Epigenetics and Stem Cells at the Helmholtz Zentrum München, Germany, Maria Elena Torres-Padilla co-chaired the 11th edition of the summit, which took place in Dalian between 27 and 29 June and was attended by more than 2000 of communicating research results and the integ- Extensive and reliable funding promoting scien- participants from 80 countries. rity of the scientific process to wider society. tific excellence will be essential to support future Under this year’s theme “Achieving Inclusive “Co-chairing the AMNC was an honour and leaders of research and development, both in Growth in the Fourth Industrial Revolution”, a great opportunity to meet with individuals academia and industry.” Torres-Padilla took the issue of funding basic committed to making a positive impact on the research to the global stage, highlighting its world,” said Torres-Padilla. “Thorough basic importance for drug discovery and technologi- research is essential for scientific advancements cal innovation, and their positive implications in the future and something that policymakers on society. She also highlighted the importance need to be aware of to ensure it is protected.

BOOK REVIEW The Mystery of Human Aging

n his book The Mystery of Human Aging, of whether a ‘cure’ for aging is a reality. “In former EMBO Fellow Björn Schumacher recent years, there has been a veritable explo- Ifrom the CECAD Research Center, University sion of new knowledge about aging,” says of Cologne, Germany, describes the biological Schumacher. “And that is what this book is insights that are transforming our understand- about.” ing of the causes of aging and human disease. “The author explains in clear terms and for a broad audience what we know about the molecular, cellular and physiological basis of The Mystery of Human Aging – Surprising aging,” says Jan Vijg, Albert Einstein College of insights from a science that’s still young Medicine, New York, USA. “Björn takes you by Björn Schumacher the hand and guides you through a wondrous Algora Publishing | March 2017 world of the accomplishments of biomedical www.algora.com/518/book/details.html research through the ages.” ISBN: 978-1628942828 The book begins with a historical excursion, looking at early descriptions of aging – from the Bible to Greek mythology – and the initial scientific studies. Throughout the remainder of the book, Schumacher covers all aspects of aging and research into the molecular mechanisms underlying it, ending with an exploration

n 5 July 2017, EMBO Secretary General Sir Paul Nurse officially opened the University ©Steve Haywood Photography Oof Exeter’s Living Systems Institute (LSI). The brainchild of EMBO Member and Deputy Vice-Chancellor Research and Knowledge Transfer, Nick Talbot, the LSI is located in a state-of-the-art collaborative research facility in which biologists, mathematicians, physicists and engineers can work together. This integration is Steven West, Phil Ingham, Paul Nurse, Christiane Nüsslein-Volhard, Maria Leptin designed to foster innovative, interdisciplinary and David Ish-Horowicz at the institute’s opening symposium. research into the fundamental molecular and cellular processes underlying living systems and the diseases that afflict them. A variety of complementary analytical meth- we can visualise and interpret our systems in Fifteen new faculty have been recruited from ods and platforms including hydrogen-deuteri- ways that we had not previously imagined.” leading international institutions to join existing um exchange mass spectrometry, cryo-electron A two-day symposium to mark the official faculty under the leadership of EMBO Member microscopy, X-ray crystallography, nanophoton- opening of the LSI included EMBO Director Philip Ingham. These include former EMBO ics, super resolution microscopy and microfluid- Maria Leptin, former EMBO Secretary General Young Investigator Tom Richards and current ics underpin the work carried out at the institute. Christiane Nüsslein-Volhard and EMBO Member EMBO Young Investigator Steve West. Research Steve West says: “The LSI vision of bringing Dame Amanda Fisher among the speakers. interests range from neural circuit structure together researchers from many disciplines under and function through stem cell self-renewal and one roof brings with it opportunities beyond the differentiation, organelle structure and function, boundaries set by my own expertise. Although to the population dynamics and interactions of we are only a few months in, we are already talk- micro-organisms and their hosts. ing to physicists and mathematicians about how

BOOK REVIEW Protein actions explained

rotein Actions: Principles and Modeling computer science to use their skills and knowl- is a new textbook by EMBO Member Ivet edge to do research in quantitative biology,” P Bahar from the University of Pittsburgh she explains. School of Medicine, USA Together with her colleagues Robert L. Jernigan, Iowa State University, USA and Ken A. Dill, Stony Brook University, USA she presents an overview of protein structure and function. Bahar says: “We Protein Actions: Principles and Modeling give examples of the power of simple models Ivet Bahar, Robert L. Jernigan, Ken A. Dill and methods, while also giving a glimpse of Garland Science, Taylor & Francis Group | challenges awaiting future researchers.” February 2017 Bahar presented the book, which is aimed at www.garlandscience.com/product/ graduates, advanced undergraduates and those isbn/9780815341772 looking for an introduction to proteins, for the ISBN: 978-0-8153-4177-2 first time in February 2017 at the Biophysical Society Meeting in New Orleans. “I wanted to write the sort of book I could have read when I first got interested in biological problems; a book that could inspire graduate students from chemical engineering, chemistry, physics, or

Awards of Excellence EMBO MEMBERS

Royal Medal Gabor Medal Spinoza Prize Danish crowns awarded by the 2018 to Piet Gros from Utrecht Novo Nordisk Foundation. University in the Netherlands for Mel Greaves, The Institute of The Gabor Medal 2017 was EMBO members Alexander his fundamental contributions Cancer Research, London, UK, awarded to Richard Durbin van Oudenaarden, Utrecht Albert Lasker Basic Medical to understanding the comple- from the University of University and Hubrecht received the Royal Society’s Research Award ment system-mediated innate Institute, The Netherlands, and Royal Medal in biological Cambridge, UK. He receives immune response. The prize is Albert Heck, Utrecht University, Michael N. Hall, Biozentrum sciences for his research on the medal and a prize of 2,000 endowed with 100,000 Swedish The Netherlands, were among Basel, Switzerland, was surface antigens that defined pound sterling for his outstand- kroner. four recipients of the Spinoza honoured with the Lasker Award the cellular lineage of different ing contributions to computa- Prize. The prize, which is for basic medical research for leukaemias. In addition to a tional biology, and their impact EMBO YOUNG INVESTIGATORS awarded by the Netherlands discoveries concerning TOR silver gilt medal, he will receive across many areas of the life proteins and their central role Organisation for Scientific IBRO Kemali Prize for Research a prize of 10,000 pound sterling. sciences. in the metabolic control of cell Research (NWO), is the most Guillermina López-Bendito, growth. The award is one of four Helmholtz International prestigious science prize in the Institute of Neuroscience, Buchanan Medal annual prizes that recognize Netherlands. They will receive Alicante, Spain, received the Fellow Award contributions to the understand- Peter Ratcliffe of the University 2.5 million euros each to be IBRO Dargut and Milena Kemali The Helmholtz Association ing, diagnosis, treatment, and of Oxford, UK, received the used for scientific research. International Prize for Research honoured Nektarios prevention of human disease. It 2017 Buchanan Medal, which in the field of Basic and Clinical Tavernarakis, Foundation for is endowed with 250,000 US is awarded by the Royal Society Martin Gibbs Medal Neurosciences for her work on Research and Technology-Hellas, dollars. for distinguished contributions Ralph Bock, Max Planck mechanisms of axon guidance Greece, with the Helmholtz in brain development, and in to the biomedical sciences and Institute of Molecular Plant Ernst Schering Prize International Fellow Award. It is endowed with 2,000 pound Physiology, Potsdam, Germany, particular in thalamocortical honours his research in an area The Ernst Schering Prize 2017 connectivity. The prize, which is sterling. Ratcliffe receives the was awarded the 2017 Gibbs of relevance to the Helmholtz has been awarded to Elly awarded to researchers under award for ground-breaking Medal for his research on Association’s work. In addi- Tanaka from the Institute of the age of 45 who have made horizontal gene transfer and research on oxygen sensing and Molecular Pathology in Vienna, important contributions in tion to 20,000 euros prize experimental evolution. The signalling pathways mediating money, Tavernarakis is invited Austria for her outstanding the field of basic and clinical medal is awarded biennially by research in the field of regenera- cellular responses to hypoxia. to become a visiting research neuroscience, is endowed with the American Society of Plant tion biology. The 50,000 euro fellow at one or more Helmholtz 25,000 euros. Francis Crick Medal and Biologists. Bock will receive prize is awarded annually by the Centers. Lecture a medal and is invited to Ernst Schering Foundation to Iain T Boyle Award convene a Martin Gibbs Medal Lwoff Medal recognize pioneering research The European Calcified Tissue Miratul Muqit, University of Symposium. that has resulted in new, inspir- Society has awarded its Iain Dundee, UK, was awarded the Jeff Errington, Newcastle ing models or led to funda- Boyle Award to Carmine Royal Society’s Francis Crick University, UK, received the Novo Nordisk Prize mental shifts in biomedical Settembre, Telethon Institute of Medal and Lecture 2018 in Lwoff Medal at the 7th Congress The 2017 Novo Nordisk knowledge. Genetics and Medicine, Naples, recognition of his research on of European Microbiologists in Prize was awarded to Poul Italy. The award recognizes cell signalling linked to neuro- Valencia, Spain. The medal is Nissen from Aarhus University, Gregori Aminoff Prize in young scientists who have made degeneration in Parkinson’s offered by the Federation for Denmark, for his pioneering Crystallography significant progress and disease. He will receive a bronze European Microbiology Societies studies of the structure and The Royal Swedish Academy of contribution to the field of bone medal and a prize of 2,000 to recognize outstanding service function of ion pumps. The prize Sciences awarded the Gregori and calcified tissue. Settembre pound sterling. to microbiology in Europe. is accompanied by 3 million Aminoff Prize in Crystallography receives a prize of 1,000 euros.

Good Read – Publications from the EMBO community An evolutionarily conserved Effector CD8+ T cell-derived Structural Basis of the Human A Unique Microglia Type Modulation of Autophagy pathway controls proteasome interleukin-10 enhances liver Endoglin-BMP9 Interaction: Associated with Restricting by BDNF Underlies Synaptic homeostasis immunopathology Insights into BMP Signaling Development of Alzheimer's Plasticity Anne Bertolotti (EMBO Member) Matteo Iannacone (EMBO Young and HHT1 Disease Nektarios Tavernarakis (EMBO and Adrien Rousseau (EMBO Investigator) and colleagues Luca Jovine (EMBO Young Ido Amit (EMBO Member) and Member) and colleagues Fellow) Journal of Hepatology | 5 May 2017 Investigator) and colleagues colleagues Cell Metabolism | 5 July 2017 Nature | 11 August 2016 Doi: 10.1016/j.jhep.2017.04.020 Cell Reports | 30 May 2017 Cell | 15 June 2017 Doi: 10.1016/j.cmet.2017.06.005 doi:10.1038/nature18943 Doi: 10.1016/j.celrep.2017.05.011 Doi: 10.1016/j.cell.2017.05.018 An Ancient Pseudoknot in Metaphase chromosome PKR activation and eIF2α Signalome-wide RNAi screen Structural Basis of Egg TNF-α Pre-mRNA Activates structure is dynamically phosphorylation mediate identifies GBA1 as a positive Coat-Sperm Recognition at PKR, Inducing eIF2α human globin mRNA splicing maintained by condensin mediator of autophagic cell Fertilization Phosphorylation that Potently at spliceosome assembly I-directed DNA (de)catenation death Luca Jovine (EMBO Young Enhances Splicing Raymond Kaempfer (EMBO Raquel Oliveira (EMBO Adi Kimchi (EMBO Member) and Investigator) and colleagues Raymond Kaempfer (EMBO Member) and colleagues Installation Grantee) and colleagues Cell | 15 June 2017 Member) and colleagues Cell Research | 4 April 2017 colleagues Cell Death and Differentiation | 2 June Doi: 10.1016/j.cell.2017.05.033 Cell Reports | 5 July 2017 eLife | 6 May 2017 Doi: 10.1038/cr.2017.39 2017 Doi: 10.1016/j.celrep.2017.06.035. Doi: 10.7554/eLife.26120 Doi: 10.1038/cdd.2017.80 Dynamic changes in murine Global survey of the forebrain miR-211 expression Multipotent peripheral glial Selectivity determinants of immunomodulatory potential Dynamic changes in murine associate with cholinergic cells generate neuroendocrine GPCR-G-protein binding of common drugs forebrain miR-211 expression imbalances and epileptiform cells of the adrenal medulla M. Madan Babu (EMBO Member) associate with cholinergic activity Giulio Superti-Furga (EMBO Igor Adameyko (EMBO Young and colleagues imbalances and epileptiform Member) and colleagues Hermona Soreq (EMBO Member) Investigator) and colleagues Nature | 18 May 2017 activity Nature Chemical Biology | 24 April 2017 and colleagues Science | 7 July 2017 Doi: 10.1038/nature22070 Doi: 10.1038/nchembio.2360 Hermona Soreq (EMBO Member) PNAS | 20 June 2017 Doi: 10.1126/science.aal3753 and colleagues Doi: 10.1073/pnas.1701201114 Mapping the human DC lineage Clonally stable Vk allelic choice instructs Igk repertoire PNAS | 6 June 2017 through the integration of Doi: 10.1073/pnas.1701201114 Geometrical frustration Genome-wide identification high-dimensional techniques Yehudith Bergman (EMBO yields fiber formation in and expression profiling of long Florent Ginhoux (EMBO Young Member) and colleagues Human fetal dendritic cells self-assembly non-coding RNAs in auditory Investigator) and colleagues Nature Communications | 30 May 2017 promote prenatal T-cell Martin Lenz (EMBO Young and vestibular systems Doi: DOI: 10.1038/ncomms15575 immune suppression through Science | 4 May 2017 Investigator) and colleagues Karen Avraham (EMBO Member) arginase-2 Doi: 10.1126/science.aag3009 Nature Physics | 3 July 2017 and colleagues Florent Ginhoux (EMBO Young Doi: 10.1038/nphys4184 Scientific Reports | 17 August 2017 Investigator) and colleagues Doi: 10.1038/s41598-017-08320-3 Nature | 14 June 2017 Doi: 10.1038/nature22795

Practical Courses Workshops IT-Siena | 25–29 August 2018 | C.T. DE-Heidelberg | 10–13 September Baldari 2018 | J. Knoblich ES-Barcelona | 12–17 November 2017 PT-Ericeira | 17–21 November 2017 | Lymphocyte antigen receptor Organoids: Modelling organ | E. Sabidó P. Domingos signalling development and disease in 3D Targeted proteomics: Experimental Proteostasis culture design and data analysis IT-Pavia | 9–12 September 2018 | A. ES-Tenerife| 16–20 January 2018 | E. Mattevi DE-Heidelberg | 16–19 September DE-Heidelberg | 20–24 November 2017 Karatekin Enzymes, biocatalysis and chemical 2018 | P. Bork | M. Paulsen Exocytosis and endocytosis: From biology: The new frontiers The human microbiome The fundamentals of high-end cell synaptic vesicles to nanodiscs sorting GR-Kyllini | 17–21 September 2018 | DE-Heidelberg | 3–6 October 2018 | A. SG-Singapore | 22–24 January 2018 | Z. Lygerou Ephrussi CH-Basel | 26 November–1 December J. Hiscox DNA replication, chromosome The complex life of RNA 2017 | C. Genoud Modelling infectious diseases in the segregation and fate decisions Volume electron microscopy by cell and host automated serial SEM CH-Arosa | 21–25 September 2018 | T. TW-Taipei | 2–6 March 2018 | C.T. Chien Simmen Global Exchange Lecture CL-Quintay | 9–21 January 2018 | J. Neural development Membrane contact sites in health Course Ewer and disease Developmental biology DE-Heidelberg | 18–21 March 2018 | SG-Singapore | 6–14 December 2017 | C. Gross DK-Copenhagen V | 2–5 October 2018 D. Svergun UK-Cambridge | 5–9 February 2018 | Microglia 2018 | L. Pedersen Structural and biophysical methods R. Salek Cilia 2018 IL-Rehovot | 8–11 April 2018 | I. Ulitsky for biological macromolecules in Metabolomics bioinformatics for life solution scientists Noncoding RNAs in embryonic IT-Capri | 14–17 October 2018 | M.R. development and cell differentiation Matarazzo IN-New Delhi | 18–29 March 2018 | From epigenome towards R. Natesh CH-Les Diablerets | 8–11 April 2018 | epitranscriptome in cell fate choice India|EMBO Symposium CEM3DIP 2018: of macromolecular G.P. Dotto assemblies and cellular tomography Perspectives on skin cancer DE-Heidelberg | 17–20 October 2018 IN-Bhubaneswar | 11–13 December prevention | K.R. Patil 2017 | S. Chauhan IT-Siena | 6–12 April 2018 | P. Experimental approaches to Autophagy: Cellular mechanism(s) Ricciardi-Castagnoli DE-Heidelberg | 15–17 April 2018 | P. evolution and ecology using yeast and significance in health and disease Molecular interrogation of single- Falter-Braun and other model systems cells to decipher population From networks to mechanisms to heterogeneity and plasticity models IT-Lucca | 21–25 October 2018 | M. Lemberg DE-Heidelberg | 9–13 April 2018 | A. SG-Singapore | 17–20 April 2018 | G.V. Endoplasmic reticulum function in EMBO Research Leadership Hendrix Shivashankar health and disease Courses Extracellular vesicles: From biology to Nuclear mechano-genomics DE-Leimen | Various dates biomedical application PT-Troia | 1–6 May 2018 | S. Boulton DE-Heidelberg | 23–30 April 2018 | J.E. Telomere biology in health and EMBO | EMBL Symposia González-Pastor human disease DE-Heidelberg | 12–14 November 2017 Microbial metagenomics: A 360º IT-Naples | 6–9 May 2018 | R. Ricci | J. Zaugg approach Lysosomes and metabolism Upcoming From single- to multiomics: GR-Heraklion | 6–17 May 2018 | A. GR-Heraklion | 8–12 May 2018 | E. Applications and challenges in data deadlines Stamatakis Seiradake integration Computational molecular evolution Molecular neurobiology EMBO Young Investigators DE-Heidelberg | 11–14 March 2018 | FR-Grenoble | 12–19 May 2018 | M. T. Hiiragi 1 April FR-Strasbourg | 15–19 May 2018 | L. 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THE EMBO EMBO JOURNAL Molecular Medicine

ARTICLE AND REPORT

No more TREM2-bling RESEARCH ARTICLE

A gene called triggering receptor Pinpointing protein RESEARCH ARTICLE expressed on myeloid cells 2, or communities RESEARCH ARTICLE TREM2, has been associated No BEACH, no hearing Proteins rarely work alone. Only Memory mechanisms with Alzheimer’s disease and other neurodegenerative diseases. through the assembly to protein The Lipopolysaccharide-responsive Two groups, Thornton et al. and complexes can they fulfill their Individuals suffering from post- beige-like anchor protein (LRBA) Schlepckow et al., now shed light cellular functions. Moreover, there traumatic stress disorder (PTSD) is known to play an important role on the role of TREM2 in normal are additional layers of functional are more prone to acquiring in the immune response. A study brain function and suggest a new organization: higher-order Alzheimer’s disease in later life. by Vogl et al., published in EMBO therapeutic target in Alzheimer's assemblies of multiple protein A study by Agís-Balboa et al., Reports, shows an additional role disease treatment. complexes, referred to as protein published in The EMBO Journal, of LRBA in auditory function. In sheds light on the molecular communities. They ensure the mice, LRBA deficiency leads to TREM2 is active in the cell mechanism that links the two efficient transfer of substrates along progressive hearing loss. A closer membrane of specialized brain disorders. enzymatic pathways, the effective look at the cellular function of immune cells called microglia. transduction of signals, and the Mice lacking the Formin 2 protein LRBA revealed that it is required Microglia use TREM2 to detect synthesis of proteins according to show symptoms reminiscent of to maintain hair bundles in the dying cells or lipids associated the local cellular needs. PTSD at an early age and acquire hair cells of the inner ear. LRBA with toxic protein aggregates. age-related memory decline. The belongs to a class of proteins that Subsequently, TREM2 is cut in In a study published in Molecular researchers propose that developing contain a so-called BEACH domain. two. The external part is shed Systems Biology, Kastritis et al., PTSD via a process that involves These proteins have previously from the protein and released, have developed a protocol to Formin 2 could, over time, cause been implicated in the assembly of while the part remaining in the identify and characterize protein an aberrant activation of many macromolecular complexes. The cell membrane is degraded. The communities in Chaetomium genes that eventually contribute new data on LRBA function are researchers uncovered that a rare thermophilum, a thermophilic to Alzheimer’s. Indeed, whereas consistent with this model. mutant, which increases the risk of filamentous fungus that is ideal Alzheimer’s disease, was cleaved for structural biology analysis young mice lacking Formin 2 were Patients with mutations in the more rapidly than the wildtype because of its superior biochemical hardly different from normal mice, LRBA gene suffer from severe version. These results suggest that stability. The researchers identified a deregulation of hundreds of genes immunodeficiency, but there stabilizing TREM2, by making it 27 distinct protein communities built up as they aged. had thus far been no mention less susceptible to cleavage, may be that include 108 interconnected These results from animal studies of hearing loss in patient a viable therapeutic strategy. complexes, which dynamically are likely to be relevant to humans. data. However, a closer look at associate with each other. The The research team showed that two patients revealed hearing TREM2 shedding by cleavage at the H157-S158 bond is accelerated for the methodology developed in the impairments in humans as well, Formin 2 is deregulated in PTSD Alzheimer’s disease-associated H157Y study complements the emerging and in patients with Alzheimer’s although less severe than in mice. variant single-cell structural biology disease. It may thus be possible to Such hearing loss could gain more Peter Thornton, Jean Sevalle, Mike J Deery, Graham Fraser, Ye Zhou, Sara Ståhl, Elske approaches that provide high- importance in the clinical setting develop therapeutic strategies for H Franssen, Roger B Dodd, Seema Qamar, resolution snapshots of subcellular PTSD patients that, at the same if the development of treatment Beatriz Gomez Perez-Nievas, Louise SC features but are currently unable time, lower the risk for developing methods allows patients to survive Nicol, Susanna Eketjäll, Jefferson Revell, Clare Jones, Andrew Billinton, Peter H St to pinpoint the underlying longer. Alzheimer’s disease. George-Hyslop, Iain Chessell, Damian C biomolecular entities. The BEACH protein LRBA is required for Crowther Formin 2 links neuropsychiatric Capturing protein communities by hair bundle maintenance in cochlear hair Read the paper: embomolmed.embo- phenotypes at young age to an increased structural proteomics in a thermophilic cells and for hearing press.org/content/early/2017/08/29/ risk for dementia eukaryote Christian Vogl, Tanvi Butola, Natja Haag, emmm.201707672 Roberto Carlos Agís-Balboa, Paulo Pinhero, Panagiotis L Kastritis, Francis J O'Reilly, Torben J Hausrat, Michael G Leitner, Michel Nelson Rebola, Cemil Kerimoglu, Eva An Alzheimer associated TREM2 variant Thomas Bock, Yuanyue Li, Matt Z Rogon, Moutschen, Philippe P Lefèbvre, Carsten Benito, Michael Gertig, Sanaz Bahari- occurs at the ADAM cleavage site and Katarzyna Buczak, Natalie Romanov, Speckmann, Lillian Garrett, Lore Becker, Javan, Gaurav Jain, Susanne Burkhardt, affects shedding and phagocytic function Matthew J Betts, Khanh Huy Bui, Wim J Helmut Fuchs, Martin Hrabe de Angelis, Ivana Delalle, Alexander Jatzko, Markus Kai Schlepckow, Gernot Kleinberger, Akio Hagen, Marco L Hennrich, Marie-Therese Sandor Nietzsche, Michael M Kessels, Dettenhofer, Patricia A. Zunszain, Andrea Fukumori, Regina Feederle, Stefan F Mackmull, Juri Rappsilber, Robert B Russell, Dominik Oliver, Matthias Kneussel, Manfred Schmitt, Peter Falkai, Julius C. Pape, Lichtenthaler, Harald Steiner, Christian Peer Bork, Martin Beck, Anne-Claude W Kilimann, Nicola Strenzke Elisabeth B. Binder, Christophe Mulle, Haass Gavin Read the paper: embor.embopress. Andre Fischer & Farahnaz Sananbenesi Read the paper: embomolmed.embo- Read the article: msb.embopress.org/ org/content/early/2017/09/18/ Read the paper: emboj.embopress.org/cgi/ press.org/content/early/2017/08/29/ content/13/7/936 embr.201643689 doi/10.15252/embj.201796821 emmm.201707672

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