{"id":53306,"date":"2022-11-16T12:00:00","date_gmt":"2022-11-16T11:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=53306"},"modified":"2022-11-18T11:09:50","modified_gmt":"2022-11-18T10:09:50","slug":"awards-honours","status":"publish","type":"embletc","link":"https:\/\/www.embl.org\/news\/embletc\/issue-99\/awards-honours\/","title":{"rendered":"Awards & honours"},"content":{"rendered":"\n

Rolf Apweiler<\/strong>, director of EMBL-EBI, has been elected a Member of the Academia Europaea<\/a>, in recognition of his status as a leading expert in his field. Academia Europea promotes European research, advises governments and international organisations in scientific matters, and furthers interdisciplinary and international research.<\/p>\n\n\n\n

Ewan Birney<\/strong>, EMBL Deputy Director General and Joint Director of EMBL-EBI, has received an honorary doctorate in bioinformatics from the University of Tartu<\/a> for his remarkable work in the development of bioinformatics and genomics, as well as his contributions to the formation and promotion of Estonian researchers.<\/p>\n\n\n\n

Miki Ebisuya, <\/strong>Group Leader at EMBL Barcelona, Cornelius Gross, <\/strong>Interim Head of EMBL Rome, <\/strong>and Nassos Typas<\/strong>, Group Leader and Senior Scientist at EMBL Heidelberg, have been elected to EMBO Membership<\/a>. It is a lifelong honour that allows elected scientists to serve on EMBO\u2019s council and committees, evaluate applications for EMBO funding, and act as mentors to young scientists.<\/p>\n\n\n\n

Anne Ephrussi<\/strong>, Director of EMBL\u2019s International Centre for Advanced Training and Senior Scientist, has been elected as one of the 150 new members of the US National Academy of Science<\/a>, for her work on the compartmentalisation and regulation of RNA molecules and localised determinants in development.<\/p>\n\n\n\n

Kai Fenzl<\/strong>, Postdoctoral Fellow in the Steimentz group, won the Otto-Schmeil Prize<\/a> for his joint work with Matilde Bertolini from Stanford University on the formation of protein complexes in human cells. This biannual prize awards young scientists for outstanding work in biological and medical research. <\/p>\n\n\n\n

Eileen Furlong<\/strong>, Head of the Genome Biology Unit and Senior Scientist, has been elected as a Fellow of the Royal Society<\/a>, for her contributions to developmental genomics and research on genome regulation during embryonic development. The Royal Society aims to recognise, support and promote science and its benefit to humanity. She <\/strong>has also  received the Gottfried Wilhelm Leibniz Prize 2022<\/a> from the German Research Foundation (DFG) in recognition of her exceptional research.  <\/p>\n\n\n\n

Wim Hagen<\/strong>, Senior Engineer in Electron Microscopy in the Mattei Team at EMBL Heidelberg, and Ardan Patwardhan<\/strong>, Team Leader at EMBL-EBI, won the Royal Microscopical Society Scientific Achievement Award<\/a>. This award recognises their contributions to the field of electron microscopy.<\/p>\n\n\n\n

Edith Heard<\/strong>, EMBL Director General, has been awarded an Honorary Doctorate by the University of Cambridge<\/a> and been elected as a foreign member of the Royal Danish Academy of Sciences and Letters<\/a>, in recognition of her academic excellence. The former distinction recognises her work in epigenetics and developmental biology. In addition, she <\/strong>has been nominated Ordinary Academician<\/a> by the Pontifical Academy of Sciences, a supranational academy of sciences whose mission is to honour pure science, ensure its freedom, and encourage research for the progress of science. She <\/strong>has also been awarded with the Richard Benz medal<\/a> for her contributions to Heidelberg as a centre of science and research.<\/p>\n\n\n\n

Matthias Hentze<\/strong>, EMBL Director and Senior Scientist, has been awarded the Centenary Award by the Biochemical Society<\/a>, for his excellent contributions in the field of biosciences and commitment to building, supporting, and nurturing talent.<\/p>\n\n\n\n

Antonia Lock<\/strong>, Scientific Database Curator at EMBL-EBI, has won the Excellence in Biocuration Award<\/a> in the Advance Career Award category. This award recognises biocurators who have been involved in a biocuration relevant field for 7 to 15 years. In her career, Antonia developed standards to describe metadata for genome-wide HTP data sets, mapped controlled vocabularies to ontologies, and done ground-work curation for a genetic disorder with drugs currently in clinical trial.<\/p>\n\n\n\n

Julia Mahamid<\/strong>, Group Leader and Senior Scientist, has received the Oswalt Foundation\u2019s Frankfurter Biophysics Prize<\/a> for her contribution to advances in electron tomographic and imaging of cells.<\/p>\n\n\n\n

John Marioni<\/strong>, Visiting Research Group Leader at EMBL-EBI, has been elected as a Fellow of the  UK Academy of Medical Sciences<\/a>, for his significant work in biomedical science. The Academy\u2019s main goal is to help in the creation of an open and progressive research sector to improve health.<\/p>\n\n\n\n

Andr\u00e9 Mateus<\/strong>, Postdoctoral Fellow at the Savitski Team  and the Typas Group, has won the Karl Freundenberg Prize<\/a> for his work on characterising the proteomic landscape of Escherichia coli<\/em>. This Prize acknowledges the work of young scientists in the field of natural sciences in the German region of Baden-W\u00fcrttemberg.<\/p>\n\n\n\n

Diana Ordo\u00f1ez<\/strong>, Head of the Flow Cytometry Core Facility, has been elected a SRL Emerging Leader in Flow Cytometry<\/a>, by the International Society for Advancement of Cytometry (ISAC) for the period 2022-2025. This nomination recognises her leadership potential and technical expertise.<\/p>\n\n\n\n

Nicoletta Petridou<\/strong>, Group Leader, has received the GfE Hilde Mangold <\/a>Early Career Award 2022 from the German Society of Developmental Biologists (GfE). <\/p>\n\n\n\n

Janet Thornton<\/strong>, Group Leader and Senior Scientist, has been selected as the inaugural winner of the Federation of European Biochemical Societies (FEBS) Journal Open Science Award<\/a>, for her lifelong commitment to open science, the key role she played in the development of the ELIXIR infrastructure<\/a> for the life sciences, and her work on developing many freely available databases and tools.<\/p>\n","protected":false},"excerpt":{"rendered":"

The work and excellence of EMBL researchers have been recognised with multiple awards and honours during the past year.<\/p>\n","protected":false},"author":120,"featured_media":53992,"parent":0,"menu_order":0,"template":"","tags":[],"class_list":["post-53306","embletc","type-embletc","status-publish","has-post-thumbnail","hentry"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"article_intro":"

The work and excellence of EMBL researchers have been recognised with multiple awards and honours during the past year.<\/p>\n","related_links":false,"source_article":false,"in_this_article":false,"press_contact":"None","article_translations":false,"languages":"","embletc_issue":[{"ID":53290,"post_author":"124","post_date":"2022-11-16 12:00:00","post_date_gmt":"2022-11-16 11:00:00","post_content":"","post_title":"Issue 99","post_excerpt":"","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"issue-99","to_ping":"","pinged":"","post_modified":"2022-11-17 11:34:48","post_modified_gmt":"2022-11-17 10:34:48","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc-issue&p=53290","menu_order":0,"post_type":"embletc-issue","post_mime_type":"","comment_count":"0","filter":"raw"}],"embletc_in_this_issue":[{"ID":53292,"post_author":"124","post_date":"2022-11-16 12:00:00","post_date_gmt":"2022-11-16 11:00:00","post_content":"\n

The minimal cell<\/h2>\n\n\n\n

In 1944, researchers from California\u2019s Department of Public Health managed to isolate the causative agent for atypical pneumonia, a respiratory illness that afflicted many military personnel during World War II. First called the \u2018Eaton Agent\u2019 after the researcher who isolated it, the pathogen was believed for many years to be an unidentified virus. It was not until the 1960s that scientists determined conclusively that the infectious agent causing atypical pneumonia was not a virus, but a very small bacterium.  <\/p>\n\n\n\n

Mycoplasma pneumoniae, <\/em>as the species was later named, is among the tiniest free-living microorganisms on Earth. Its genome contains only 687 genes. For comparison, Escherichia coli<\/em>, the bacteria most commonly used in lab studies, has over 4,400 genes, while human beings have over 20,000. At less than 1 micron in length, 1.5 trillion M. pneumoniae<\/em> could fit into a single droplet of water. When it infects humans, it parasitises respiratory tract cells, often evading the immune system during the process. Also, unusual for bacteria, it lacks a cell wall surrounding its plasma membrane. <\/p>\n\n\n\n

A group of EMBL scientists is now using this unique organism to interrogate fundamental processes that underlie the biology of a living cell. Spearheaded by the research group of Julia Mahamid<\/a>, and enabled by collaborations with multiple groups within and outside EMBL, the researchers are attempting to 'see', at unprecedented resolution, the mechanisms of life inside one of the smallest living cells.\u00a0\u00a0<\/p>\n\n\n\n

From pathogen to model<\/strong><\/h2>\n\n\n\n

Researchers from EMBL\u2019s Structural and Computational Biology unit established Mycoplasma pneumoniae <\/em>as a model organism in the early 2000s. Teams led by Peer Bork<\/a>, Luis Serrano<\/a>, and Anne-Claude Gavin<\/a> sequenced and annotated its genome, which was followed by the publication of three seminal papers delineating its metabolomics, proteomics, and transcriptomics, respectively.\u00a0<\/p>\n\n\n\n

Two decades earlier, Jacques Dubochet<\/a>, another EMBL researcher, had developed a way to prepare and image biological samples using cryo-electron microscopy (cryo-EM), work that won him the Nobel Prize in 2017. Relying on a method of freezing biological samples extremely quickly to prevent the formation of ice crystals, cryo-EM allows researchers to observe the structure of complex biomolecules at atomic resolution.\u00a0<\/p>\n\n\n\n

Soon afterwards, researchers developed the technique of cryo-electron tomography (cryo-ET), another big leap in harnessing the power of electron microscopy. While cryo-EM allows scientists to observe the structure of biological molecules, it usually requires samples of carefully isolated molecules taken out of their cellular context. However, cryo-ET allows scientists to take snapshots of intact cells, along with all their internal components, which can later be reconstructed in 3D. <\/p>\n\n\n\n

Given Mycoplasma\u2019s <\/em>small size, it is possible to obtain a series of images to combine into a clear picture of the entire cell and all its constituents. When Mahamid started her group at EMBL in 2017, she decided to harness the growing power and resolution of advanced cryo-ET technologies to study cellular mechanisms in action inside this model organism.<\/p>\n\n\n\n

\u201cPersonally, I'm amazed by the ability to do structural biology inside cells,\u201d said Joe Dobbs, one of the PhD students in the Mahamid group. \u201cCryo-EM is well-known for its ability to provide insight into the structures of macromolecular complexes in purified samples, but actually seeing the insides of cells, and how molecules interact with each other in context, is incredible.\u201d<\/p>\n\n\n\n

\"Female
Julia Mahamid, Group Leader in the Structural and Computational Biology Unit, EMBL Heidelberg, in front of a Titan Krios cryo-electron microscope. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n\n\n\n

Connecting biology across scales<\/strong><\/h2>\n\n\n\n

The study has attracted a diverse group of scientists and engineers. Vastly differing in areas of interest and expertise, they are united by their belief in the potential for M. pneumoniae <\/em>to serve as a window into the life of a cell. <\/p>\n\n\n\n

For example, Judith Zaugg<\/a> started her lab at EMBL in 2014 and is interested in understanding the molecular basis of complex genetic traits and diseases, for which she usually works with human genomics data. With Mycoplasma, <\/em>she became fascinated by the idea of observing gene expression in action within a living cell. In the cryo-ET images that the Mahamid group grabs, DNA can be observed as filamentous structures and the RNA polymerase enzymes seen attached to them, and Zaugg believes that one day this might be used to figure out which regions of DNA or genes are active \u2013 or being \u2018transcribed\u2019 \u2013 at a given point in time.\u00a0<\/p>\n\n\n\n

\u201cIt is very exciting to \u2018see\u2019 transcription in progress,\u201d said Zaugg. \u201cWith this model, we can perhaps one day address very fundamental biological questions like \u2013 how does the cell reorganise its DNA upon receiving a certain stimulus? While we know (based on genomics data) that genes are differentially expressed based on stimuli, we still don't know how the cell rearranges its internal structure and genome to achieve this.\u201d  <\/p>\n\n\n\n

\"Two
Judith Zaugg, Group Leader in the Structural and Computational Biology Unit, EMBL Heidelberg, and Frosina Stojanovska, PhD student in the Zaugg lab, looking at a computationally annotated M. pneumoniae tomogram. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

With future advances in correlative electron and fluorescence microscopy, Zaugg hopes that answering questions like these might become possible. In turn, her team brings to the project computational expertise to mine the data, which otherwise could have taken months or even years to process.<\/p>\n\n\n\n

Peer Bork<\/a>, who co-initiated and coordinated the initial proteomic, transcriptomic, and metabolomic characterisation of M. pneumoniae <\/em>in the 2000s, is interested not only in the infectious disease aspects of this model system but also in its potential for understanding molecular networks. His group has aided the study with computational expertise as well as by connecting global bioinformatic data.\u00a0<\/p>\n\n\n\n

\u201dThis project leverages some of EMBL\u2019s key strengths \u2013 collaborating and coordinating across a diversity of disciplines to answer fundamental biological questions that cannot be addressed otherwise,\u201d said Bork. <\/p>\n\n\n\n

Maria Zimmermann-Kogadeeva<\/a>, another EMBL group leader, started collaborating with Mahamid while still a postdoc in the Bork group. Her computational insights played a key role in a recent project that studied the machinery of protein synthesis in action inside the cell. She is also involved in a project focused on studying previously uncharacterised membrane proteins that can be observed in cryo-ET images of Mycoplasma.\u00a0<\/em><\/p>\n\n\n\n

\u201c<\/em>The cryo-ET technology allows us to look deep inside the cell, and understand how intracellular processes change under different conditions,\u201d said Zimmermann-Kogadeeva. \u201cThe data obtained is of very high quality and can be combined with other molecular datasets to ask interesting questions.\u201d She and Bork are both optimistic about the potential of investigating cellular metabolomics within Mycoplasma<\/em> in the future. <\/p>\n\n\n\n

\u201cOur goal is to connect biology across scales,\u201d said Mahamid. \u201cMycoplasma <\/em>gives us a way to study biological systems all the way across from the nanometre range of molecules to the micrometre range of entire cells.\u201d <\/p>\n\n\n\n

New tools for new insights<\/strong><\/h2>\n\n\n\n

While cryo-ET allows scientists to look at the whole cell, it doesn\u2019t make it easy to identify what<\/em> they are seeing. Unlike with fluorescence microscopy,  it isn't easy to tag or label specific objects inside the cell and distinguish them from their neighbours in cryo-ET. As a result, scientists are effectively left with an incomplete map, most of which has no helpful labels. <\/p>\n\n\n\n

Soheil Mojiri, a postdoctoral fellow in the Ries group<\/a>, is building a microscope to solve this problem. An engineer by training, Mojiri is fascinated by the possibility of exploiting optical physics to address challenging biological questions. His goal is to fruitfully marry cryo-ET and super-resolution optical microscopy at low temperatures.\u00a0<\/p>\n\n\n\n

\"Two
Jonas Ries, Group Leader in the Cell Biology and Biophysics Unit, EMBL Heidelberg and Soheil Mojiri, postdoc in the Ries group, in front of Mojiri\u2019s prototype cryo-single molecule localisation microscope (cryo-SMLM). Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cCryo-ET allows us to look at molecular architecture and molecules in context, but we're limited by what we can identify in the extremely noisy, crowded, and heterogeneous cellular environment. So while we can just about make out big things, such as ribosomes - the cell's protein production machines, smaller molecules and complexes can escape our notice unless we have prior information to use,\u201d said Mojiri. <\/p>\n\n\n\n

Mojiri is developing a prototype microscope that would allow scientists to take a frozen cell sample, visualise individual proteins or complexes with fluorescent tags that are genetically introduced into live cells, and later subject the same sample to cryo-ET. Comparing the images obtained by the two methods would let researchers leverage electron microscopy\u2019s structural resolution as well as fluorescence microscopy\u2019s specificity. <\/p>\n\n\n\n

Not all technology development for this project is on the hardware side, however. The researchers have generated a huge volume of data, which presents challenges in analysing it to draw new insights. This is where Anna Kreshuk<\/a>, with her expertise in machine-learning-based image analysis, steps in. Kreshuk and her team create innovative AI-based methods that find meaningful information from biological images, often gigabytes in size and containing a lot of background information that may not be relevant.\u00a0<\/p>\n\n\n\n

\"Three
Anna Kreshuk (centre), Group Leader in the Cell Biology and Biophysics Unit, with Jonas Ries (right) and Julia Mahamid (left). Credit: Jervis Thevathasan \/ EMBL <\/figcaption><\/figure>\n\n\n\n

Ricardo Sanchez, an ARISE fellow<\/a> at EMBL Heidelberg, has been working on finding ways around this challenge. \u201cWith cryo-ET, one of the biggest problems is reducing the signal-to-noise ratio and identifying structures of interest among all the cellular background,\u201d he said. \u201cMy goal is to solve this problem with the least amount of computational resources.\u201d<\/p>\n\n\n\n

\u201cWhat fascinates me is the completeness of this system,\u201d said Kreshuk. \u201cIt's the whole living thing. Everything that it needs to be an independent (and pretty dangerous) living organism is visible in that one image.\u201d<\/p>\n\n\n\n

Putting together a cellular picture<\/strong><\/h2>\n\n\n\n
\"The
Using cryo-ET, researchers can look at small bacteria in progressively higher resolutions, ultimately resolving the structure of molecular machines, such as ribosomes. From left to right, this graphic shows M. pneumoniae <\/em>cells being placed on a grid for cryo-electron microscopy, a cryo-ET slice of the cell with ribosomes marked in green, and the resolved structure of an individual ribosome derived from such an image. In the background, we can see M. pneumoniae cells, as seen using scanning electron microscopy. Credit: Isabel Romero Calvo \/EMBL<\/figcaption><\/figure>\n\n\n\n

The project is already yielding dividends when it comes to understanding fundamental biological processes that make life possible. In a recently published paper, Liang Xue from the Mahamid group led a study that allowed the team to visualise the process of translation \u2013 the synthesis of new proteins \u2013 inside the cell at atomic detail. The structures they focused on is probably one of the easiest to identify in a cryo-ET image \u2013 ribosomes. Ribosomes are some of the most ancient molecular machines present in all living organisms and essential for protein synthesis. <\/p>\n\n\n\n

\u201cRibosomes not only play an essential role in genetic information flow but also serve as platforms to monitor cellular states, e.g. cell stress response,\u201d said Xue. \u201cInside living cells, ribosomes function as highly interconnected networks of molecular machines.\u201d <\/p>\n\n\n\n

Using high-quality cryo-ET Mycoplasma <\/em>data, <\/em>the researchers were not only able to observe the dynamic structural changes that took place in ribosomes as they proceeded through the protein synthesis cycle, but they could also observe what happens to these processes when antibiotics perturb cells. Since the translation machinery is quite similar in structure and function throughout the tree of life, the study can be extrapolated to other prokaryotic or eukaryotic species that are more challenging to image with cryo-ET. <\/p>\n\n\n\n

\"Two
Liang Xue, postdoc, and Joe Dobbs, PhD student in the Mahamid group, at the Titan Krios electron microscope controls. Julia Mahamid and Rasmus Kjeldsen Jensen can be seen in the background. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cI hope my work at EMBL establishes a framework<\/a> to do high-resolution<\/a> structural biology inside the cell,\u201d said Xue. \u201cRibosomes and Mycoplasma<\/em> are just the beginning. With more and more molecular machines resolved inside cells, we are heading toward the ultimate goal of building an atomic cell model.\u201d<\/p>\n\n\n\n

Collaborating to make progress<\/strong><\/h2>\n\n\n\n

The researchers are also using Mycoplasma <\/em>to understand the role of unknown membrane proteins that can be observed in cryo-ET images In these studies, Jan Kosinski<\/a>\u2019s and Christian L\u00f6w<\/a>\u2019s groups at EMBL Hamburg and Nassos Typas<\/a>\u2019s group at EMBL Heidelberg are also involved. A tool they have turned to often in these investigations is AlphaFold<\/a>, the AI algorithm that predicts protein structures, whose developers won the 2023 Breakthrough Prize in life sciences.\u00a0<\/p>\n\n\n\n

The project also involves collaborations with scientists outside EMBL and in EMBL member states, including the groups of J\u00f6rg St\u00fclke<\/a>, Georg-August-Universit\u00e4t G\u00f6ttingen, Patrick Cramer<\/a>, Max Planck Institute for Multidisciplinary Sciences, Juri Rappsilber<\/a>, Institut f\u00fcr Biotechnologie, Technische Universit\u00e4t Berlin, and Luis Serrano<\/a>, Centre for Genomic Regulation, Barcelona.<\/p>\n\n\n\n

While research in the last few decades has helped to rapidly identify and annotate many species\u2019 genomes, our knowledge of the function and precise roles of most genes and proteins remains incomplete, even for an organism as simple as Mycoplasma<\/em>. Projects like these are a key step towards bridging this knowledge gap. EMBL\u2019s new programme \u2018Molecules to Ecosystems\u2019<\/a> aims to study living organisms in the context of their environment. In doing so, scientists will doubtless encounter many more new molecules and biological processes, which this project paves the way towards studying and understanding in detail. It also exemplifies the collaborative approaches at the heart of this new programme.<\/p>\n\n\n\n

\"A
Rasmus Kjeldsen Jensen, postdoc in the Mahamid group, working in the lab. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cI think it is a pretty long and hard way from imaging Mycoplasma<\/em> to the data interpretation. We need diverse expertise and knowledge to pave this way,\u201d said Mojiri. \u201cIn particular, we require biologists, physicists, and data scientists.\u201d The collaborative atmosphere at EMBL has made such a coming together of talents and knowledge possible. The team gathers in a monthly meeting dedicated to the Mycoplasma<\/em> project to exchange ideas, discuss the progress of experiments, and troubleshoot challenges.<\/p>\n\n\n\n


\u201cMycoplasma <\/em>has turned out to be a powerful model for studying the dynamics of molecular machines and understanding intracellular cross-talk,\u201d said Mahamid. \u201cThe collaborative approach was absolutely crucial to this. To realise the massive potential of cryo-ET and the Mycoplasma <\/em>model, we will need to continue as we have started, together and moving forward.\u201d<\/p>\n","post_title":"Uncovering a microbe\u2019s inner life","post_excerpt":"Researchers have observed the inner workings of an unusual bacteria at an unprecedented level of detail.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"uncovering-a-microbes-inner-life","to_ping":"","pinged":"","post_modified":"2022-11-16 14:36:13","post_modified_gmt":"2022-11-16 13:36:13","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=53292","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":53294,"post_author":"124","post_date":"2022-11-16 12:00:00","post_date_gmt":"2022-11-16 11:00:00","post_content":"\n

When a team of EMBL biologists decided to conduct an expedition to Iceland earlier this year to collect environmental samples from its coast, a volcano was not really in the plan. But when Fagradalsfjall, located 60 km from Reykjavik, erupted only five days before the expedition, it added a little bit of otherworldliness to a trip which had already been pushing at the boundaries of \u2018traditional\u2019 fieldwork.  <\/p>\n\n\n\n

\"Photograph
The Fagradalsfjall volcano erupted on 3 August 2022, five days before the expedition was due to start. Many of the expedition members made the short trip froom their sampling location to the volcanic site for a once-in-a-lifetime experience. Credit: Niko Leisch\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cIt was absolutely breathtaking,\u201d recalls Joanna Zukowska, a scientist in the Pepperkok team<\/a> at EMBL Heidelberg. \u201cI was speechless.\u201d<\/p>\n\n\n\n

The expedition was the final pilot for Traversing European Coastlines (TREC)<\/a>, a flagship project of the new EMBL programme that aims to study life in context. TREC is a way to bring together environmental research and molecular and cellular biology to address urgent societal challenges.<\/p>\n\n\n\n

Over a period of three weeks in August 2022, EMBL researchers and their collaborators visited three different locations in Iceland \u2013 Reykjavik, Westfjords, and Akureyri \u2013 with unique climatic and environmental conditions. They collected marine organisms, soil, seawater, and sediments, and tested out experimental protocols that would become critical for the large-scale expedition that EMBL will run in 2023 and 2024 for the TREC project. <\/p>\n\n\n\n

\"Map
Map of Iceland showing the chief sampling sites. The three primary locations are shown in orange, and secondary sites in black. Credit: Kiley Seitz\/EMBL, Map data: Google Earth \u00a9<\/strong>2022. <\/figcaption><\/figure>\n\n\n\n

This pilot expedition was co-organised by the Icelandic biodiversity research network BIODICE. It involved collaborations with host institutions across Iceland, including the Marine and Freshwater Research Institute (MFRI) and the University of Iceland. <\/p>\n\n\n\n

Skimming for Plankton<\/strong><\/h2>\n\n\n\n

Reykjavik is the capital of Iceland and home to the Marine and Freshwater Research Institute (MFRI)<\/a>. This institute was the first stop for the EMBL researchers and their collaborators for this pilot expedition. The visit was supported by MFRI\u2019s director \u00deorsteinn Sigur\u00f0sson and marine geneticist Christophe Pampoulie.<\/p>\n\n\n\n

Preparations began last year when EMBL scientists visited Iceland to engage with the local scientific community, visit institutes, and check out sampling locations.  This summer, the TREC team shipped scientific equipment, labware, and reagents to MFRI, a vast logistics effort coordinated by Cristian Tambley, Valerie Maier, Niko Leisch, and Paola Bertucci at EMBL.<\/p>\n\n\n\n

The sample-collecting teams soon followed. <\/p>\n\n\n\n

\"A
EMBL Team Leader Yannick Schwab holding up a plankton net. Credit: \u00a9Kristinn Ingvarsson\/University of Iceland<\/figcaption><\/figure>\n\n\n\n

Once at the site, the teams quickly settled into a routine. Every morning began with climbing into a boat and heading out to the ocean. Once a safe distance from shore, a plankton net \u2013 a specially constructed cone-shaped net with an extremely fine mesh \u2013 was thrown overboard and dragged behind the boat for a few minutes. This allowed enough time for it to fill with tiny unicellular sea creatures called plankton, which the team then filtered and carried back to shore. Once back at MFRI\u2019s labs, the teams went to work, studying and preserving the plankton in various ways.<\/p>\n\n\n\n

\u201cPlanktons fill the oceans and seas around us and yet we know so little about them,\u201d said Omaya Dudin<\/a>, group leader at the Swiss Federal Institute of Technology Lausanne (EPFL) and one of the members of the expedition. \u201cThey're extremely important for the oxygenation of the planet, for the food chain in the sea, and for the climate and the environment.\u201d<\/p>\n\n\n\n

\"Photograph
The boat which carried researchers to plankton sampling sites each morning. Credit: Hiral Shah\/EMBL <\/figcaption><\/figure>\n\n\n\n

Dudin\u2019s lab specialises in understanding the origin of animal development using expansion microscopy, a technique which they share with their collaborators \u2013  Gautam Dey<\/a>, Sinem Saka<\/a>, and Yannick Schwab<\/a> at EMBL Heidelberg and Marine Laporte, Paul Guichard, and Virginie Hamel at the University of Geneva. When an opportunity to join the TREC expeditions came up, the \u2018Expansion Team\u2019 felt it was too good an opportunity to lose. <\/p>\n\n\n\n

Expansion microscopy involves embedding biological samples in a gel matrix, and then slowly expanding the gel. The embedded cells get \u2018blown up\u2019 along with the gel, allowing scientists to glimpse details that would ordinarily have been beyond the resolution of light microscopy. It also allows better permeability for stains and antibodies, helping researchers identify structures, proteins, and molecular complexes inside the cells. <\/p>\n\n\n\n

In spite of its remarkable strengths and potential, expansion microscopy is not a technique routinely tested in the field. Members of the Expansion microscopy team who travelled to Iceland worked on standardising its protocols to observe plankton samples freshly obtained from the sea. <\/p>\n\n\n\n

\"Two
Johanna Zukowska and Karel Mocear filtering collected plankton samples on the expedition boat. Credit: Hugo Berthelot\/EMBL<\/figcaption><\/figure>\n\n\n\n

The expansion team had two goals: to create a biobank and to build an atlas of plankton images. The biobank \u2013 a catalogue of plankton species that can serve as a baseline biodiversity snapshot \u2013 would allow scientists to identify potential future changes as oceans warm over the coming years. The atlas \u2013 a collection of images grabbed by expansion microscopy of marine plankton species \u2013 would also act as an invaluable resource for future biologists. <\/p>\n\n\n\n

\u201cThere are about 10 million species estimated to live on this planet. Out of these, we have only identified or characterised about two million using genomics,\u201d said Dudin. \u201cAnd out of these millions, there are only 50 model organisms from which we have learned almost all the biology that we know today.\u201d<\/p>\n\n\n\n

Characterising and measuring the biodiversity of our shallow oceans and coastal ecosystems would be the first step towards building up a complete picture of the networks that sustain life in these incredibly vulnerable environments. <\/p>\n\n\n\n

\"A
The team that collected and processed planktons at Reykjavik. Credit: TREC Team.<\/figcaption><\/figure>\n\n\n\n

Going after invertebrates<\/strong><\/h2>\n\n\n\n

Biodiversity exists at many scales, however, and not all the creatures the biologists sought at Iceland were microscopic. Leslie Pan and Emily Savage joined the expedition representing the Arendt group<\/a> at EMBL Heidelberg and their interests lie in a small marine ragworm called Platynereis dumerilii. <\/em><\/p>\n\n\n\n

\"An
An immature Platynereis worm. Credit: Emily Savage\/EMBL<\/figcaption><\/figure>\n\n\n\n

The life cycle of Platynereis dumerilii<\/em> is linked closely to the lunar cycle. After emerging as larvae, the worms swim around in the sea until they grow large enough to \u2018settle\u2019. During this next stage, they build long tubes that attach to sea algae and rocks and live inside them until they mature. The final step takes place during new moon nights, when the mature individuals swim to the surface of the sea to mate and spawn the next generation. <\/p>\n\n\n\n

For biologists, the fascination for Platynereis dumerilli <\/em>lies in the fact that it is extremely slow evolving \u2013 it is believed to have changed little genetically and phenotypically in the last several million years. This, in turn, makes it an ideal candidate to study the evolution and emergence of the central nervous system. While it has been cultured in the lab since 1953, studying it directly in its natural environment presents many interesting opportunities. <\/p>\n\n\n\n

\"A
Emily Savage examining algae for the presence of Platynereis. Credit: Leslie Pan\/EMBL<\/figcaption><\/figure>\n\n\n\n

For the Arendt team, their days during the expedition started with loading equipment into a van and driving out to the predetermined coastal sites in Reykjavik and the Westfjords. Once there, expert divers retrieved clumps of algae from shallow sea floors. On the beach, Pan and Savage set up workstations with wide trays, where they spent the next few hours sorting through algae, searching for evidence of hidden tubes and worms within. <\/p>\n\n\n\n

While the team found no evidence of P. dumerilii <\/em>in the waters on this trip, many other invertebrate species were present. During the main TREC expedition, beginning in 2023, the team are confident to find the worms. \u201cWe plan to look at their population genetics in relation to the surrounding environmental factors, like the temperature or salinity of the seawater,\u201d said Pan. \u201cWe would like to see whether such factors have given rise to distinct genotypes and whether the genotypes, in turn, have helped them adapt better to their surroundings.\u201d<\/p>\n\n\n\n

\"Small
Planarians adhering to the surface of a rock. Credit: Hanh Vu\/EMBL<\/figcaption><\/figure>\n\n\n\n

Hanh Vu<\/a>, who joined EMBL Heidelberg as a group leader in 2021, is fascinated by another class of worms \u2013 planarians. Planarians are free-living flatworms that have almost unlimited regenerative capacity, and depending on the habitat and species, range in length from just a few millimetres to over a metre. Vu\u2019s lab studies different species of planarians to figure out how and why animals regulate their body size. <\/p>\n\n\n\n

Just like with Platynereis, <\/em>environmental conditions, such as gradients of salinity and temperatures, affect how these worms adapt to their surroundings. This brought Vu and her team to the field and to TREC, where they headed out to coastal sites where the little planarians live among fields of seagrass and algae. <\/p>\n\n\n\n

\"Photograph
Hanh Vu and her teammates at one of the sampling sites. Credit: Hanh Vu\/EMBL<\/figcaption><\/figure>\n\n\n\n

\u201cSince marine planarians tend to stick to submerged rocks, it was important for us to catch them at the right time, when the low tide exposed these rocks,\u201d said Vu. Once they spotted the critters, they used paint brushes to sweep them off the rocks and into the waiting collection tubes. In addition to marine planarians, the team also sampled from freshwater environments. <\/p>\n\n\n\n

\u201cThere are very few previous reports of marine planarians in Iceland,\u201d said Vu. \u201cUnexpectedly, we found that they were actually quite abundant at the sites where we sampled. So that was a pleasant surprise.\u201d<\/p>\n\n\n\n

Soil, sediments, and pollution<\/strong><\/h2>\n\n\n\n

This visit to Iceland was the third pilot expedition in the run-up to TREC, previous editions having taken place in Villefranche, France, and Naples, Italy. Kiley Seitz, a microbial ecologist working at EMBL Heidelberg, has been part of every pilot so far. An expert in soil microbiology, she has coordinated the sampling site selection as well as the sample collection protocols.  Along with other EMBL scientists, she collected soil, water, and sediment samples along \u2018land-sea transects\u2019 \u2013 straight line paths leading from the sea to adjoining lands. <\/p>\n\n\n\n

For this team, the sampling process began with the now-familiar procedure of loading up a car with hundreds of pre-labelled bags and tubes and travelling to predetermined sites. Once there, the teams identified representative land-sea transects and selected sampling spots at regular distances along them, moving away from the sea. <\/p>\n\n\n\n

To collect soil samples, the researchers used a \u2018corer\u2019 \u2013 a long metal tube that can be inserted into the ground at a specified depth and used to dig out a cylindrical section of soil. At each sampling spot, the researchers collected five such samples which they mixed together to form a representative picture of that position.<\/p>\n\n\n\n

\"A
Sara Verstraeten collecting a soil core while Kiley Seitz sorts through previous samples. Credit: Richard Jacoby\/EMBL<\/figcaption><\/figure>\n\n\n\n

Helping collect soil and sediment samples was Richard Jacoby, who is interested in microbial species that can degrade environmental pollutants. He plans to extract pollutants (usually pesticides, pharmaceuticals, or antibiotics) from the samples back at EMBL, and analyse them chemically. <\/p>\n\n\n\n

\u201cIf we start doing this in multiple places, in Iceland or throughout Europe, we can start to get a chemical profile of what pollutants are in each place,\u201d said Jacoby. \u201cAnd then perhaps we can start connecting these chemical datasets to other datasets, particularly those obtained by microbial genome sequencing.\u201d<\/p>\n\n\n\n

In Reykjavik, this team studied two sites -- one of which had acted as a dumping ground for many years but had later been treated with bioremediation protocols. The other was a \u2018pristine\u2019 site, but close to a few aluminium factories. The team collected soil and sediment samples from both with plans to conduct metagenomic and biochemical studies.<\/p>\n\n\n\n

In this, they were joined by Joanna Zukowska, who was also part of the plankton-collecting teams in the early days of the expedition. \u201cI have always dreamed of working in the field,\u201d said Zukowska. \u201cThis was a great opportunity for me to learn more about fieldwork and about marine biology.\u201d<\/p>\n\n\n\n

\"A
Joanna Zukowska collecting sediments from coastal waters. Credit: Richard Jacoby\/EMBL<\/figcaption><\/figure>\n\n\n\n

#WeFreezeontheBeach<\/strong><\/h2>\n\n\n\n

In 2017, EMBL alumnus Jacques Dubochet received the Nobel Prize<\/a> for developing a way to prepare and image biological samples using cryo-electron microscopy, a technique that has made it possible for researchers to study the structure of biomolecules at an unprecedented level of detail. <\/p>\n\n\n\n

\"A
A high-pressure freezer that the team took to Iceland. Credit: Yannick Schwab\/EMBL<\/figcaption><\/figure>\n\n\n\n

Now, researchers are bringing this technique from the lab into the field, greatly expanding the scope of the type of biological samples it can study. In addition to plankton and flatworm-collecting biologists, the Iceland pilot expedition team included electron microscopy specialists who tested out protocols for quickly freezing samples in field conditions (and posted their adventures on Twitter with the hashtag \u201c#WeFreezeOnTheBeach\u201d). <\/p>\n\n\n\n

\u201cIt was very important for us at this stage to consolidate the protocols \u2013 how are we going to collect the samples, store them, reference them etc.,\u201d said Yannick Schwab<\/a>, Head of the Electron Microscopy Core Facility at EMBL Heidelberg. <\/p>\n\n\n\n

One of the teams most interested in this process was that of Ben Engel<\/a> from the University of Basel, Switzerland. The Engel group studies the cellular architecture of marine algae. <\/p>\n\n\n\n

\u201cWe are trying to understand how the chloroplast harvests the energy of light to make the biochemical energy that sustains all life on Earth, and how that energy is then used for carbon fixation,\u201d said Engel. To do this, they carry out cryo-electron tomography, a technique where thin sections of frozen cells can be imaged in 3D at high resolution to reveal their inner structures. During the Iceland expedition, the team tried out some of its sample preparation steps in the field. <\/p>\n\n\n\n

\u201cThis is new. There are very few people doing cryo-electron microscopy in the field,\u201d said Anna Steyer, cryo-ET specialist at EMBL Heidelberg. \u201cWhen you think of fieldwork equipment, you think of binoculars, not of sample preparation for high-end cryo-EM. The power of this technology is opening up new questions that biologists anywhere can now address.\u201d<\/p>\n\n\n\n

The teams tested different types of freezing protocols for different applications, for example, plunge freezing for cryo-electron tomography, or high-pressure freezing for volume-electron microscopy. While for this particular expedition, required equipment was shipped beforehand to Iceland from participating institutions, eventually a truck that travels coast to coast will house the equipment needed for future fieldwork. And that\u2019s EMBL\u2019s mobile lab services. <\/a><\/p>\n\n\n\n

\"Three
Annemarie Perez Boerema and Manon Demulder plunge-freezing small algae cells on a Vitrobot, which the team brought to Iceland. Image credit: Ben Engel\/University of Basel<\/figcaption><\/figure>\n\n\n\n

\u201cThis was an excellent dry-run for what we will be facing next year during TREC,\u201d said Niko Leisch, Operational Manager-EMBL mobile services. \u201cFor me, it was important to see the different groups with different scientific aims in action. Observing their workflows yields important clues that would help us improve on planning for future trips.\u201d<\/p>\n\n\n\n

Traversing Coastal Ecosystems<\/h2>\n\n\n\n

This expedition was many years in the making. EMBL\u2019s new five-year programme \u2018Molecules to Ecosystems\u2019<\/a>, which was launched in January 2022<\/a>, laid down the ambitious goal of advancing our understanding of ecosystems at the molecular level to study life in its natural context. To help achieve this, EMBL initiated several transversal themes<\/a> which support the multidisciplinary science necessary to realise projects like these. One of these themes is Planetary Biology<\/a>, which aims to study, from the molecular to the population level, how microbes, plants, and animals respond to each other and to their environment.<\/p>\n\n\n\n

TREC, a flagship project part of the Planetary Biology theme, aims to study <\/em>coastal ecosystems across Europe and their responses to a fast-changing environment to address environmental challenges to planetary and human health. In realising this goal, EMBL\u2019s researchers and mobile services will work closely together with the Tara Ocean Foundation, the Tara Oceans Consortium (now TaraOceanS), the European Marine Biological Resource Centre (EMBRC), as well as many other national research institutions. <\/p>\n\n\n\n

\u201cGiven the scale and urgency of human and planetary health challenges, it is important for EMBL to organise this large pan-European, highly collaborative and cross-disciplinary project,\u201d said Paola Bertucci, Scientific Expedition Manager for TREC. \u201cEMBL is well positioned to lead this because of its intergovernmental status and large network of collaborators and partners.\u201d<\/p>\n\n\n\n

Throughout this pilot expedition, co-organised by the Icelandic biodiversity research network BIODICE, EMBL researchers and their collaborators interacted closely with their host institutes in Iceland, with whom they formed strong scientific connections and set up future collaborations. It was an opportunity to exchange scientific knowledge as well as expertise, as molecular biologists met marine scientists and ecologists. <\/p>\n\n\n\n

\"A
Johan Decelle from CNRS Grenoble observing a sample under a microscope. Credit: \u00a9Kristinn Ingvarsson\/University of Iceland<\/figcaption><\/figure>\n\n\n\n

\u201cWe had a very positive reaction and a lot of interest from the Icelandic scientific community, and new collaborations were formed around our technologies and scientific questions,\u201d said Leisch. \u201cThis aspect of giving back to the scientists in our member states is a very important one for me, and is one of the central missions of the mobile services.\u201d <\/p>\n\n\n\n

In addition to the scientific activities, the trip also included public engagement and outreach events. On a walk called \u201cScience on the Beach\u201d, coordinated by Sara Verstraeten, TREC Outreach & Public Engagement Manager, members of the public could engage with the expedition scientists to learn more about their work. <\/p>\n\n\n\n

\"A
Kiley Seitz giving a demonstration to visitors during \u2018Science on the Beach\u2019. Credit: \u00a9Bj\u00f6rn G\u00edslason \u2013 BGI \/University of Iceland.<\/figcaption><\/figure>\n\n\n\n

With lessons learned from Iceland, the team looks forward now to preparing for the next expeditions that will begin in France in spring 2023 <\/em>and conclude in Greece nearly 18 months later. <\/p>\n\n\n\n

\u201cIceland is always breathtaking. All day long, one is surrounded by a rather hostile, alien landscape shaped by volcanic activity,\u201d said Leisch. \u201cBut the warmth of the Icelandic people more than makes up for that.\u201d<\/p>\n","post_title":"From coast to coast and beyond","post_excerpt":"EMBL researchers conducted a pilot project in Iceland as the final preparatory step before commencing their journey traversing European coastlines.\n","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"from-coast-to-coast-and-beyond","to_ping":"","pinged":"","post_modified":"2023-02-06 15:20:52","post_modified_gmt":"2023-02-06 14:20:52","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&p=53294","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"}]},"yoast_head":"\nAwards & honours | EMBL<\/title>\n<meta name=\"description\" content=\"The work and excellence of EMBL researchers have 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