Defying the Virus Sarah-Maria Fendt and Markus Ralser Journal
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WINTER 2020/2021 ISSUE 44 How EMBO Members and their colleagues have risen to the scientific challenge Defying the virus PAGES 2-3 EMBO Gold Medal 2020 A look at the first nine months Sarah-Maria Fendt and Journal-independent Markus Ralser peer review PAGE 7 PAGE 11 Meeting report Excellence in the life sciences Homecoming Gender roles in academia The new EMBO Members Experiences from EMBO Installation Grantees PAGE 10 PAGE 13 PAGE 12 www.embo.org TABLE OF CONTENTS EMBO NEWS Defying the virus EMBO Member rising to the scientific challenge Pages 3-4 Papers, preprints, and free lunches Interview with EMBO Head of Scientific Publishing, Bernd Pulverer Page 5 Promoting best practice in European science Meeting report Obituary Reflections on ways to tackle scientific Gender roles and their impact in academia Hermann Bujard (1934–2020) – pioneering misconduct Page 10 researcher and visionary science politician Page 16 Page 6 SDash: the SourceData dashboard Accelerating collaboration Page 11 In contrast to the HCA, the group Defying the virus leaders responsible for setting up and running the Vienna Biocenter’s Across the world, scientists and clinicians have combined in extraordinary impressively efficient SARS-CoV-2 efforts to help fight the COVID-19 pandemic. Three members of the EMBO testing programme had no prior experience in community tell how they and their colleagues have risen to this scientific the field, but simply felt that they needed to help. “We had the instruments, we had extensive Around the world challenge. EMBO Gold Medal 2020 expertise in molecular biology, and we thought Recent EMBO Global Activities together with we should pool our brainpower and equipment,” Sarah-Maria Fendt and Markus Ralser awarded By Kathy Weston Associate Member States says one of them, Andrea Pauli. Page 7 Review Commons: A look at the first Page 17 In her role as co-founder of the are far easier to catch. Due to the public health Three parallel initiatives were set up: an RT-qPCR nine months Human Cell Atlas (HCA), EMBO implications, the results were fast-tracked into pipeline for in-house testing and monitoring, led by Journal-independent peer review EMBO community Member and Gold Medallist Sarah print in a much-cited paper in April 2020. Johannes Zuber, and also involving Stefan Ameres; Updates from across Europe Teichmann coordinates a network More recent data show there is good concord- next generation sequencing, led by Ulrich Elling, Page 11 Pages 18-25 of hundreds of researchers around the world. As ance between the consortium’s predictions of Luisa Cochella and Alex Stark; and RT-LAMP, led the first ominous hints that SARS-CoV-2 was no where the virus would enter, and where it is by Julius Brennecke and Pauli. Interestingly, all Installation grants Awards and publications ordinary coronavirus appeared in early 2020, the actually found. “A good example is if you map seven are either EMBL alumni, present or past © Ine Dehandschutter © Homecoming - experiences from grantees Achievements and papers by members of the HCA community mobilised. “If you have a pre- the oral cavity from healthy donors and COVID- EMBO Young Investigators, or EMBO Members. Page 12 EMBO community existing community,” Teichmann says, “people 19 patients,” says Teichmann. “There are cells in They were joined by many other volunteers from Page 26 know each other, and they are very willing to the salivary glands that have high expression of the Vienna Biocenter research community. EMBO Membership collaborate”. From her laboratory at the Wellcome ACE2, and when we stain in tissue sections you Neither Pauli nor Brennecke had worked on Sanger Institute in Cambridge, Teichmann asked can see the virus sitting there.” anything related to LAMP (loop-mediated isother- her fellow researchers to use their published and To accompany their ongoing COVID-19 work, mal amplification) technology before. “I’m a “The award highlights that our research unpublished data to generate a map delineating the HCA community now maintains an open zebrafish embryologist and Julius works on RNA on metabolism and metastasis THE where in the body a panel of genes involved in access data portal, containing reference data from biology in flies, and to be honest, I didn’t even know formation is important” EMBO viral uptake was expressed. many more healthy tissues, together with single what LAMP was in March!” Pauli laughs. However, JOURNAL Interview with EMBO Gold Medallist It soon became clear from the pooled data that cell mapping of patient sample data, and spatial LAMP proved to be the best solution to developing Sarah-Marie Fendt one of the reasons for SARS-CoV-2’s rapid trans- mapping data from infected post-mortem tissue. a cheap and robust assay that could also be used in Page 8 missibility was the presence of the viral receptor The portal has become an invaluable resource, lower- and middle-income countries, where uncer- ACE2 and its associated protease TMPRSS2 on accessed tens of thousands of times. “It’s really tain supply chains and limited equipment make cells in the nose, mouth, upper airways and eyes; helped me get through this terrible year to know testing for SARS-CoV-2 especially challenging. this may explain why some respiratory viruses that we’ve been able to contribute something The assay costs less than 1€ per reaction, and Lifetime honour for 63 leading scientists like SARS-CoV-2 and influenza, whose receptors useful,” Teichmann says. only requires simple reagents and a waterbath Pages 13-14 are more highly expressed in the upper airways, set at 63ºC. An open-access version with home- © Janie Airey © Fresh from EMBO Press made enzymes is available, and Pauli hopes it Four of EMBO Press‘ latest publications at will be adopted not only in Austria, where diag- EMBO Members in the spotlight a glance Surprising moments that influenced their nostics labs and hospitals are now recommended Page 27 research “People know each other, to use it for testing, but worldwide. Page 15 Of the testing programme in general, Pauli EMBO events and they are very willing emphasizes that it was a team effort: “The whole Upcoming courses, workshops and courses campus has come together, from the directors, Page 28 to collaborate” “It feels great that metabolism is back particularly Harald Isemann (managing direc- tor of the IMP), to the students and technicians in focus” Sarah Teichmann running the assays. To some extent, the pandem- Interview with EMBO Gold Markus Ralser ic pushed us apart, but this project has really Page 9 brought us together.” photo courtesy of Sebastian Nevols 2 EMBOencounters | Winter 2020/2021 | [email protected] ©2020 EMBO ©2020 EMBO EMBOencounters | Winter 2020/2021 | [email protected] 3 EMBO NEWS EMBO NEWS In addition to his academic research, Vivier is also Chief Scientific Officer of Innate Pharma, Papers, preprints, and free lunches which had acquired Avdoralimab, an anti-C5a drug which had already passed phase 1 trials, Biologist Bernd Pulverer, Head of Scientific Publication at EMBO, discusses papers, some years previously. Aided by a French govern- preprints, academic presses, and the curse of the journal impact factor ment grant, Innate has provided the drug gratis to be tested against placebo in an ongoing Interview conducted by Thiago Carvalho Photo courtesy of IMP/Benedikt Mandl Photo courtesy of IMP/Benedikt double-blind randomised trial. Results are yet to be published, but Vivier is cautiously opti- Let’s jump right in. Why isn’t The EMBO Journal a mistic. “This is a potential path,” he says. “I’m fully open access journal? not saying that it’s definitely going to work—it That’s a very good question, because we have may not—but we may provide some treatments three open access journals, and one does wonder for patients who need them. And that would why they are not all open access. The reason is that be extraordinary.” our journals are quite expensive because they are highly selective and because the selection is based on in-depth editorial- and peer-review. It costs about 10,000 euros to produce a single published article. In the traditional open access model, the Life science author pays directly from whatever source they researchers’ efforts can find, and often this would unfortunately be “The pandemic pushed us their research budgets. This increasingly is flip- apart, but this project has to fight ping to a model where institutions or funders pay. In the institutional subscription model that The really brought us together” COVID-19 EMBO Journal and EMBO Reports have, this cost is distributed to many more readers. Andrea Pauli In April 2020, EMBO invited its 1800 Members Bernd Pulverer and 150 Young Investigators to report on Why do open access fees vary between different any efforts they or their institutions are From left to right: Ulrich Elling, Luisa Cochella, Johannes Zuber, Stefan Ameres, Alexander Stark EMBO Press publications? making to help fight the ongoing COVID- (at rear), Harald Isemann, Andrea Pauli, and Julius Brennecke. We’re trying to price our open access journals “Do not use journal-based metrics, such as journal Springer Nature, where at the end of the day what- 19 pandemic. We received responses from at an equitable level, and we are cross-financing impact factors, as a surrogate measure of the qual- ever project you do has to have a profit-compati- close to 400 scientists, of which 328 reported these journals from our subscription journals. ity of individual research articles, to assess an indi- ble business plan. Three examples of projects that SARS-CoV-2-related activities of their own Five years ago, EMBO Member 40 molecules for which drugs had already been That’s why we’ve kept two journals hybrid, and vidual scientist’s contributions, or in hiring, promo- don’t have a business model are preprints, set research groups, of their institutions, or their Eric Vivier co-founded Marseille developed in other contexts.