{"id":58539,"date":"2023-05-15T12:00:00","date_gmt":"2023-05-15T10:00:00","guid":{"rendered":"https:\/\/www.embl.org\/news\/?post_type=embletc&#038;p=58539"},"modified":"2023-05-15T12:23:23","modified_gmt":"2023-05-15T10:23:23","slug":"can-the-effects-of-the-environment-cross-generations","status":"publish","type":"embletc","link":"https:\/\/www.embl.org\/news\/embletc\/issue-100\/can-the-effects-of-the-environment-cross-generations\/","title":{"rendered":"Can the effects of the environment cross generations?"},"content":{"rendered":"\n<p>One of the most fundamental questions in biology is how our basic traits are transmitted across generations \u2013 from parents to offspring. Researchers at EMBL Rome are now investigating this question in the light of novel epigenetic mechanisms discovered in recent years, and from the perspective of understanding disease risks.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>A focus on epigenetic inheritance at EMBL Rome<\/strong><\/h2>\n\n\n\n<p>Embryonic development begins when egg and sperm cells fuse to form the zygote. During this process, genetic information, in the form of DNA sequences, is passed on to the next generation through chromosomes derived from both parents.&nbsp; Parental chromosomes also carry epigenetic information \u2013 chemical modifications to the DNA or its associated proteins \u2013 that can affect gene expression without changing the DNA sequence.&nbsp;<\/p>\n\n\n\n<p>Relative to the DNA sequence, this inherited epigenetic information is more susceptible to being modified by the parental environment (e.g. diet), which, in turn, could potentially affect the embryo adversely. To guard against this, the newly-formed embryo undergoes a process known as <strong>epigenome reprogramming<\/strong>, which erases most of the epigenetic information inherited from parents, acting as a \u2018hard reset\u2019. However, scientists have recently found that some epigenetic information escapes reprogramming, allowing for <em>intergenerational<\/em> epigenetic inheritance that can influence the traits of the offspring.<\/p>\n\n\n\n<p>At present, we know very little at the molecular level about how epigenetic factors delivered by the egg or sperm cells can cause such intergenerational changes. The groups of <a href=\"https:\/\/www.embl.org\/groups\/hackett\/\">Jamie Hackett<\/a> and <a href=\"https:\/\/www.embl.org\/groups\/boskovic\/\">Ana Boskovic<\/a> at EMBL Rome are trying to elucidate the molecular mechanism(s) of intergenerational epigenetic inheritance by focusing on different steps of the process and using complementary approaches.<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"539\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-02-28-at-15.14.01-1024x539.png\" alt=\"Two scientists, female and male, photographed outdoors.\" class=\"wp-image-59023\" srcset=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-02-28-at-15.14.01-1024x539.png 1024w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-02-28-at-15.14.01-300x158.png 300w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-02-28-at-15.14.01-768x404.png 768w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-02-28-at-15.14.01.png 1906w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"vf-figure__caption\">Ana Boskovic (left) and Jamie Hackett (right). Credit: Eyl\u00fcl G\u00f6ker\/Shosho<\/figcaption><\/figure>\n\n\n\n<p>Over the last few years, the Hackett group made important contributions to the field by performing <a href=\"https:\/\/www.embl.org\/news\/science\/unravelling-epigenetic-reprogramming\/\">large-scale genetic screening<\/a> to delete thousands of genes in turn and identify those involved in epigenetic reprogramming.&nbsp;<\/p>\n\n\n\n<p>\u201cWe have identified two genes (Dppa2 and Dppa4) that are only switched on during very early development but are required to establish the correct epigenetic state of important developmental genes,\u201d said Hackett. \u201cIn <a href=\"https:\/\/www.embl.org\/news\/science\/a-metaphor-for-epigenetic-inheritance\/\">more recent work<\/a>, we observed that Dppa2 also has a safeguarding role to prevent transmission of abnormal epigenetic modifications to offspring.\u201d<\/p>\n\n\n\n<p>A common research interest in the Boskovic and Hackett groups is how the paternal environment, i.e. the conditions experienced by the father, can have an impact on reproduction and inheritance. The two groups use different paradigms to perturb the paternal environment: altering the diet of the father (Boskovic group) or changing the composition of the paternal gut microbiome (Hackett group). In both cases, the aim is to understand how such environmentally-induced changes in epigenetic information can influence gene expression patterns in the embryo, and therefore contribute to the health status of the next generation.<\/p>\n\n\n\n<figure class=\"vf-figure wp-block-image size-large\"><img loading=\"lazy\" decoding=\"async\" width=\"1024\" height=\"586\" class=\"vf-figure__image\" src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-03-14-at-12.27.41-1024x586.png\" alt=\"Female scientist in lab coat working on a microinjection setup.\" class=\"wp-image-59025\" srcset=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-03-14-at-12.27.41-1024x586.png 1024w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-03-14-at-12.27.41-300x172.png 300w, https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/Screenshot-2023-03-14-at-12.27.41-768x439.png 768w\" sizes=\"auto, (max-width: 1024px) 100vw, 1024px\" \/><figcaption class=\"vf-figure__caption\">Ana Boskovic performing microinjections in blastocysts. Credit: Eyl\u00fcl G\u00f6ker\/Shosho<\/figcaption><\/figure>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Making use of local resources and expertise<\/strong><\/h2>\n\n\n\n<p>Paternal effects following a variety of environmental exposure paradigms are studied across the world and the interest in the phenomenon of intergenerational epigenetic inheritance in mammals has gathered widespread excitement over the last decade. However, differences in setups and contexts may sometimes lead to confounding results, leaving many questions about this process with unclear answers.&nbsp;<\/p>\n\n\n\n<p>\u201cEMBL Rome has deep expertise in epigenetic inheritance research and in developing environmental exposure paradigms that can be studied in a systematic manner, by precisely controlling genetic and environmental conditions,\u201d said Boskovic. \u201cWithin the Epigenetics and Neurobiology Unit, we can also rely on the support from state-of-the-art local facilities. For example, the Laboratory Animal Resources (LAR) at EMBL Rome comprises a gnotobiotic facility \u2013 a sterile environment \u2013 housing germ-free mice. These mice are extremely valuable for intergenerational epigenetic inheritance studies, since they allow control over the specific composition of gut microbiota.\u201d<\/p>\n\n\n\n<p>The local expertise in gene editing technologies also helps scientists to address specific questions and needs. In particular, a study from the Hackett group resulted in the development of a powerful epigenome editing tool that allows dynamic programming of chromatin modifications at specific genomic loci, to study their inheritance and role in development and disease. The tool is being used for many epigenetic research projects at the site and will be further implemented to understand the direct impact of epigenetic modifications, supported by the recent <a href=\"https:\/\/www.embl.org\/news\/lab-matters\/erc-consolidator-grant-success-at-embl\/\">ERC Consolidator Grant awarded to Jamie Hackett<\/a>.<\/p>\n\n\n\n<h2 class=\"wp-block-heading\"><strong>Human-relevant environments<\/strong><\/h2>\n\n\n\n<p>Looking forward, a common goal of the Hackett and Boskovic groups is to widen the context of their studies on intergenerational epigenetic inheritance, to include all three major environmental modalities: biological, physical, and social. The main aim is to better understand the scope of environmental inputs on animal physiology, reproductive fitness and offspring phenotypes in mammals.<\/p>\n\n\n\n<p>This question is the core of an ongoing project that the two groups are coordinating within the <a href=\"https:\/\/www.embl.org\/about\/programme\/research-plans\/human-ecosystems\/\">Human Ecosystem Transversal Theme<\/a>, one of the research areas defined by the current <a href=\"https:\/\/www.embl.org\/about\/programme\/\">EMBL Programme \u2018Molecules to Ecosystems\u2019<\/a>. The approach is to establish different paradigms of human-relevant environmental perturbations, including the three main environmental modalities: biological, physical, and social.&nbsp;<\/p>\n\n\n\n<p>Gut microbiome dysbiosis is a paradigm of a perturbed biological environment; physical environments perturbations may include diet or pharmaceuticals, while social environments can be influenced by induced stress. This study will be conducted in a controlled environment in mice, integrating age and genetic background as contextual parameters, to assess the resulting impact of a perturbed environment on progeny.&nbsp;<\/p>\n\n\n\n<p>The molecular findings obtained from this study will be integrated with epidemiological data resulting from human cohort studies. Ultimately, this will help clarify the intricate relationship between environmental exposures and disease burden in human populations across generations.&nbsp;<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Scientists at EMBL Rome are developing new paradigms to study the impact of diverse environmental factors on reproduction in mammals and disease risk in their progeny.<\/p>\n","protected":false},"author":92,"featured_media":58739,"parent":0,"menu_order":0,"template":"","tags":[14295,39,498,514],"class_list":["post-58539","embletc","type-embletc","status-publish","has-post-thumbnail","hentry","tag-boskovic","tag-epigenetics","tag-hackett","tag-rome"],"acf":{"featured":true,"show_featured_image":false,"field_target_display":"embl","field_article_language":{"value":"english","label":"English"},"article_intro":"<p>Scientists at EMBL Rome are developing new paradigms to study the impact of diverse environmental factors on reproduction in mammals and disease risk in their progeny.<\/p>\n","related_links":[{"link_description":"Boskovic group","link_url":"https:\/\/www.embl.org\/groups\/boskovic\/"},{"link_description":"Hackett group","link_url":"https:\/\/www.embl.org\/groups\/hackett\/"}],"source_article":false,"in_this_article":false,"press_contact":"None","article_translations":false,"languages":"","embletc_issue":[{"ID":58531,"post_author":"124","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"","post_title":"Issue 100","post_excerpt":"","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"issue-100","to_ping":"","pinged":"","post_modified":"2023-05-15 13:01:59","post_modified_gmt":"2023-05-15 11:01:59","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc-issue&#038;p=58531","menu_order":0,"post_type":"embletc-issue","post_mime_type":"","comment_count":"0","filter":"raw"}],"embletc_in_this_issue":[{"ID":58537,"post_author":"104","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"<!-- wp:paragraph -->\n<p>Have you ever wondered how groundbreaking new scientific technologies come into being?<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Or how scientists and engineers work together to push the frontiers of innovation?&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>We caught up with several members of EMBL Grenoble\u2019s technology-related teams, who opened their doors to give us a sneak peek into this process of innovation. Their skills and collaborative strengths are demonstrated aptly by one of their latest projects: <a href=\"https:\/\/www.embl.org\/news\/lab-matters\/two-in-one-combining-massif-1-and-crystaldirect\/\">the complete automation of an integral step<\/a> in X-ray crystallography, a technique used by scientists worldwide to determine the 3D structures of proteins and other macromolecules.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:heading -->\n<h2><strong>Synergies driving innovation<\/strong><\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph -->\n<p>EMBL Grenoble has been <a href=\"https:\/\/www.embl.org\/news\/lab-matters\/structural-biology-at-embl\/\">at the forefront of technological developments<\/a> in the field of structural biology for three decades. This expertise has been built over time thanks to collaborative work between structural biologists and engineers.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Franck Felisaz, a mechanical engineer in the team of Gergely Papp, joined EMBL in the mid-nineties to work on instrumentation projects. \u201cThe early days of instrumentation at EMBL Grenoble involved what were pretty much craft projects, based on progressive iterations,\u201d explained Felisaz. \u201cThe teams were not structured like they are today, but there was a family-type work environment, where engineers would talk with the scientists over a cup of coffee about the challenges they faced.\u201d&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>According to Felisaz, such informal interactions often led to creative solutions to issues scientists face in their work. He referred to this interactive and problem-solving spirit as a \u201cvirtuous circle creating a trustful relationship between engineers and scientists\u201d \u2013 something that still persists at EMBL Grenoble.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":58919,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/image-80-1024x683.png\" alt=\"Two male engineers working with lab equipment. \" class=\"wp-image-58919\"\/><figcaption class=\"wp-element-caption\">Franck Felisaz, a mechanical engineer in the Papp team, and Marcos Lopez Marrero, former mechatronics engineer in the Papp team, at the MASSIF-1 beamline. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>With the opening of the European Synchrotron Radiation Facility (ESRF) next to EMBL Grenoble in 1994, the use of X-ray-based techniques for determining the structure of macromolecules became popular with structural biologists. EMBL Grenoble started to jointly operate crystallography beamlines dedicated to structural biology with the ESRF, through the Joint Structural Biology Group (JSBG).<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Macromolecular crystallography allows scientists to examine the structure of crystallised macromolecules by bombarding them with X-rays. However, the process involved many challenges.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>\"Scientists realised in the late nineties that manual operations were a real bottleneck,\u201d said Felisaz, who was already thinking of automating processes back then. \u201cI had been discussing with them for some time about how we would reduce the time wasted and inaccuracies that result from manual manipulations.\u201d<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>This need for technological improvements came at the same time as Florent Cipriani taking over the leadership of engineering activities at EMBL Grenoble, and the decision to create separate instrumentation and synchrotron teams. \u201cBenefitting from experiences from the industrial world, the newly structured instrumentation team at EMBL Grenoble started to offer solid and appropriate solutions for structure determination based on macromolecular crystallography,\u201d said Felisaz.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>The team started to develop prototype instruments allowing reliable and reproducible automation of processes. These innovations included, among other things, sample holder standards (to hold crystals and facilitate robotic handling), sample changers (to handle crystals), and goniometers (to present the crystals to the X-ray beam), and were real game-changers for scientists who rapidly adopted them. Many were also commercialised for use all around the world.&nbsp;&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Felisaz explains that the innovation cycle doesn\u2019t stop here: once a technology has been adopted by scientists, they will eventually find new ways of using it for their research and, together with engineers, arrive at opportunities to take it to the next level.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:heading -->\n<h2><strong>Combining technologies<\/strong><\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph -->\n<p>One of the recent additions to the portfolio of EMBL inventions is the CrystalDirect<sup>TM <\/sup>technology, originally developed by the Marquez and Cipriani teams in EMBL Grenoble. This technology streamlines the preparation of crystals for diffraction experiments and makes it possible to integrate crystallisation and synchrotron data collection into a continuous experimental workflow than can be controlled and operated over the internet.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>The CrystalDirect<sup>TM <\/sup>technology is currently implemented at the crystallisation facilities at EMBL Grenoble and EMBL Hamburg, and has been utilised by hundreds of users from academia and industry around the world.<strong> <\/strong>The integration of a CrystalDirect&#x2122;robot at the&nbsp; MASSIF-1 beam line, which offers new and exciting experimental opportunities, is a good example of the synergies between scientists and engineers at EMBL.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>This massive project involved the three technology-related teams at EMBL Grenoble: the <a href=\"https:\/\/www.embl.org\/groups\/marquez\/\">Marquez Team<\/a>, running the High-throughput crystallography platform (HTX), the <a href=\"https:\/\/www.embl.org\/groups\/mccarthy\/\">McCarthy Team<\/a>, operating the EMBL-ESRF beamlines, and the <a href=\"https:\/\/www.embl.org\/groups\/papp\/\">Papp Team<\/a>, leading the instruments development.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>It also included the Structural Biology group at the ESRF, in line with the long-standing and fruitful collaboration between EMBL Grenoble and ESRF over the last few decades through the JSBG. The project benefitted from the latest upgrade to the synchrotron in 2020 (EBS \u2013 the \u2018Extremely Brilliant Source\u2019) \u2013 which made ESRF the most powerful source of X-ray worldwide, allowing unprecedented possibilities in terms of research and technological developments.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>This project is therefore the culmination of several innovations developed in parallel at EMBL Grenoble, as it combines CrystalDirect&#x2122; \u2013 an automated crystal harvester developed in 2008 by the Marquez and Cipriani teams \u2013 and MASSIF-1 \u2013 a unique automated beamline dedicated to macromolecular crystallography, jointly developed and operated by EMBL and the ESRF.&nbsp;&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:acf\/vfwp-card {\"id\":\"block_64539a8b3194c\",\"name\":\"acf\/vfwp-card\",\"data\":{\"image_source\":\"media_library\",\"_image_source\":\"field_602ba83883d48\",\"image\":\"\",\"_image\":\"field_5ebd3243ee8ec\",\"title\":\"What is a beamline?\",\"_title\":\"field_5ebd3243ee989\",\"subheading\":\"\",\"_subheading\":\"field_603b4403d386e\",\"text\":\"Macromolecular crystallography requires a high intensity X-ray beam which is produced by a specific ring-shaped infrastructure, called a synchrotron, composed of \u2018beamlines\u2019 that use X-rays generated\u00a0 by accelerating electrons to near-light speeds in the ring.\",\"_text\":\"field_5ebd3243eea26\",\"link\":\"\",\"_link\":\"field_5ebd3243eeac3\",\"style\":\"bordered\",\"_style\":\"field_5ebd3244102b1\",\"image_ratio\":\"default\",\"_image_ratio\":\"field_61d41d4bcbbee\"},\"align\":\"\",\"mode\":\"preview\"} \/-->\n\n<!-- wp:acf\/vfwp-card {\"id\":\"block_64539ae23194d\",\"name\":\"acf\/vfwp-card\",\"data\":{\"image_source\":\"media_library\",\"_image_source\":\"field_602ba83883d48\",\"image\":\"\",\"_image\":\"field_5ebd3243ee8ec\",\"title\":\"What is crystallisation?\",\"_title\":\"field_5ebd3243ee989\",\"subheading\":\"\",\"_subheading\":\"field_603b4403d386e\",\"text\":\"To carry out diffraction experiments at a synchrotron, large numbers of crystals have to be produced and prepared for data collection. This typically happens at dedicated robotic facilities like the HTX lab in EMBL Grenoble.\",\"_text\":\"field_5ebd3243eea26\",\"link\":\"\",\"_link\":\"field_5ebd3243eeac3\",\"style\":\"bordered\",\"_style\":\"field_5ebd3244102b1\",\"image_ratio\":\"default\",\"_image_ratio\":\"field_61d41d4bcbbee\"},\"align\":\"\",\"mode\":\"preview\"} \/-->\n\n<!-- wp:acf\/vfwp-card {\"id\":\"block_64539aff3194e\",\"name\":\"acf\/vfwp-card\",\"data\":{\"image_source\":\"media_library\",\"_image_source\":\"field_602ba83883d48\",\"image\":\"\",\"_image\":\"field_5ebd3243ee8ec\",\"title\":\"What is CrystalDirect\\u0026#x2122;?\",\"_title\":\"field_5ebd3243ee989\",\"subheading\":\"\",\"_subheading\":\"field_603b4403d386e\",\"text\":\"The \\u003ca href=\\u0022https:\/\/www.embl.org\/news\/science\/1604-crystaldirect\/\\u0022\\u003eCrystalDirect\\u0026#x2122;\\u003c\/a\\u003e technology consists of an extremely precise robot that streamlines the step of crystal sample harvesting and preparation for X-ray diffraction at the beamline. It automatically harvests the biomolecular crystal from the crystallisation plate where it has been grown, and preserves the crystal sample by cryo-cooling it.\",\"_text\":\"field_5ebd3243eea26\",\"link\":\"\",\"_link\":\"field_5ebd3243eeac3\",\"style\":\"bordered\",\"_style\":\"field_5ebd3244102b1\",\"image_ratio\":\"default\",\"_image_ratio\":\"field_61d41d4bcbbee\"},\"align\":\"\",\"mode\":\"preview\"} \/-->\n\n<!-- wp:paragraph -->\n<p>\u201cCrystalDirect and MASSIF-1 were a perfect match at the perfect time,\u201d said Matthew Bowler, EMBL beamline scientist in the McCarthy team, in charge of operating MASSIF-1. Bowler joined EMBL in 2012, after spending several years at the ESRF where he started developing ideas for a fully automated beamline \u2013 MASSIF-1 \u2013 which became operational in 2012 and received a major<a href=\"https:\/\/www.embl.org\/news\/science\/grenoble-beamline-update\/\"> upgrade<\/a> in 2020.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>\u201cWhen MASSIF-1 was coming online, CrystalDirect&#x2122; was being developed. The latter started to generate a large number of crystals, and we actually had the capacity and automation to run them with MASSIF-1 without anybody having to do it manually. So the obvious next step was to marry these two technologies to have CrystalDirect&#x2122; on the beamline,\u201d added Bowler.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":58923,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/image-82-1024x683.png\" alt=\"Two male engineers working with lab equipment.\" class=\"wp-image-58923\"\/><figcaption class=\"wp-element-caption\">Matthew Bowler, EMBL beamline scientist in the McCarthy team, and Didier Nurizzo, ESRF scientist, both in charge of operating the MASSIF-1 beamline at the ESRF. Credit: Stuart Ingham\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:heading -->\n<h2><strong>Overcoming challenges<\/strong><\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph -->\n<p>This idea was first tested in 2018 as a proof of concept on another beamline, ID30B, putting together three technologies developed at EMBL Grenoble: the \u2018Flex\u2019 \u2013&nbsp; a robotic arm in charge of moving crystal samples from one place to another, the goniometer \u2013&nbsp; an instrument presenting the crystal to the beam, and CrystalDirect&#x2122; \u2013 a machine that harvests the crystal samples. They identified key issues that were likely to stall the project and would need to be resolved before integrating the CrystalDirect&#x2122; machine in the beamline.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":58921,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/image-81-1024x683.png\" alt=\"CrystalDirect harvester, with an overlay marking various important parts.\" class=\"wp-image-58921\"\/><figcaption class=\"wp-element-caption\">The CrystalDirect harvester (top right) integrated into the experimental hutch of the MASSIF-1 beamline, together with two pieces of equipment: the robotic arm \u2018Flex\u2019 (middle) to collect the crystal samples from the CrystalDirect harvester and transfer them to the goniometer for X-ray diffraction experiments, and a humidity control device (left) used for room temperature experiments. T. Credits: Stuart Ingham\/EMBL, Isabel Romero Calvo\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>After a successful proof of concept, the construction and integration phase started in 2021 on MASSIF-1, led by the Papp team \u2013 with Frank Felisaz in charge of building the machine, mechatronic engineer Marcos Lopez Marrero in charge of the electronics, and software engineer Jeremy Sinoir in charge of preparing the machine software for its integration in a beamline environment. The engineers kept the user firmly in mind during the process.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>\u201cThe experimental room of MASSIF-1 is very small, so it has been very challenging to fit everything into this space within the imposed constraints. We wanted to make sure that the ergonomy of the installation would be optimal for scientists so that they could easily handle their samples, even if it would be more complicated for the maintenance,\u201d said Felisaz.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:acf\/vfwp-embed {\"id\":\"block_645412485dea8\",\"name\":\"acf\/vfwp-embed\",\"data\":{\"url\":\"https:\/\/www.youtube.com\/embed\/MWiwuMUH5XA\",\"_url\":\"field_5ecbb005d2d93\",\"caption\":\"Credit: Victor Armijo Gomez\/EMBL\",\"_caption\":\"field_5ecbb0e7d2d94\",\"ratio\":\"16 x 9\",\"_ratio\":\"field_5ecbb0f3d2d95\"},\"align\":\"\",\"mode\":\"preview\"} \/-->\n\n<!-- wp:paragraph -->\n<p>\u201cOnce the CrystalDirect&#x2122; instrument was installed in the beamline, the project then became like a football game, requiring a lot of coordination and where everyone had to work together,\u201d said Bowler. All the scientists and engineers involved in the project had weekly meetings, as well as brainstorming and technical planning meetings, to plan the work carefully.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>\u201cThe main challenge was to get about five different pieces of hardware and five different pieces of software to work together reliably to be able to provide the service to users,\u201d explained Bowler. \u201cIt\u2019s generally the case with every beamline, but we added an extra level of complexity with the harvester; it was a huge challenge.\u201d<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Serena Rocchio, postdoctoral fellow in the McCarthy and Marquez teams, was in charge of coordinating the project. \u201cThe complexity also came with having to coordinate this new installation together with running the normal operation of the beamline,\u201d said Rocchio. \u201cThis wouldn\u2019t have been possible without the great teamwork and expertise from different backgrounds we had access to.\u201d<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Rocchio worked in close collaboration with software engineer Jeremy Sinoir from the Papp team, who made sure that all the machines\u2019 software could work together. \"There was a specific part requiring a lot of attention and meticulousness \u2013 error case management,\u201d said Sinoir. \u201cThis beamline has to work completely autonomously, so we couldn\u2019t afford any malfunctions. For each potential problem encountered, we needed to develop a recovery procedure.\u201d<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>This was achieved by integrating the harvester into <a href=\"https:\/\/mxcube.github.io\/mxcube\/\">MXCuBE<\/a>, an open-source beamline control software developed by an international consortium coordinated by the ESRF and with the CRIMS software, used to operate the HTX facility. This adaptation was done by Jean-Baptiste Florial, a Full Stack Software engineer in the McCarthy team, Peter Murphy and Raphael Bourgeas, CRIMS Software Developers in the Marquez Team, and Jeremy Sinoir in the Papp Team. This integration enables scientists to design experiments over the internet from their labs, which later on will be automatically executed at the HTX lab and at the beam line.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:acf\/vfwp-embed {\"id\":\"block_645411e65dea7\",\"name\":\"acf\/vfwp-embed\",\"data\":{\"url\":\"https:\/\/www.youtube.com\/embed\/BzGUUQoRwhA\",\"_url\":\"field_5ecbb005d2d93\",\"caption\":\"Credit: Victor Armijo Gomez\/EMBL\",\"_caption\":\"field_5ecbb0e7d2d94\",\"ratio\":\"16 x 9\",\"_ratio\":\"field_5ecbb0f3d2d95\"},\"align\":\"\",\"mode\":\"preview\"} \/-->\n\n<!-- wp:paragraph -->\n<p>Finally, the scientific validation of this new pipeline was a crucial component of all the project coordination. It offered the team the chance to integrate new experimental modalities, like data collection at room temperature \u2013 an opportunity the scientists identified before the project started and has now been implemented.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Usually, crystal samples are cryo-cooled to a temperature of 100 Kelvin (-173\u00b0C) &nbsp;to allow them to resist radiation damage from powerful X-rays that normally destroy biological material. Data collection at room temperature is thus extremely difficult to do and until now involved a laborious manual process. Since the new automated pipeline allows the crystal sample to be quickly harvested and immediately mounted on the beamline, it provides scientists an accessible and reliable way of collecting data at room temperature that can now be automated for the first time.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:heading -->\n<h2><strong>The idea becomes reality<\/strong><\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph -->\n<p>After running all the commissioning phases, the new automated \u2018protein to structure pipeline\u2019 was used for the first time on one of Bowler\u2019s and Marquez collaborative research projects with Mohamed-Ali Hakimi, a researcher at the Institute of Advanced Biosciences. The scientists are currently working on a protein from the parasite <em>Toxoplasma gondii <\/em>with the objective of developing new drugs against Toxoplasmosis. The combination of low- and room-temperature automated modalities makes this beamline unique and particularly useful when a lot of screening is required, like in the case of drug development.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>\u201cWhen we got our first sample, it worked perfectly! It was a fantastic feeling,\u201d Bowler said. \u201cWe know that this is going to support amazing research and hundreds of people across Europe will find it useful. It\u2019s very exciting\u201d. This rapid integration was made possible by years of preliminary work of Marquez, McCarthy and Papp Teams in collaboration with the ESRF Structural Biology group, which provided a solid and reliable basis for the implementation of this fully automated pipeline.&nbsp;&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":58917,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/image-79-1024x819.png\" alt=\"A close-up image of a protein crystal.\" class=\"wp-image-58917\"\/><figcaption class=\"wp-element-caption\">Crystal of the <em>Toxoplasma gondii<\/em> protein investigated by Bowler, Marquez and IAB researcher Mohamed-Ali Hakimi, using the new combination of HTX lab and MASSIF-1 capabilities. Credits: Matthew Bowler\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>This enthusiasm was shared by the engineers involved in the project. \"The first time that several of our most successful machines started working together was truly an incredible moment; we've never done that before!\u201d said Sinoir.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>\"We made a unique and super-optimised beamline,\u201d added Felisaz. \u201cWe were able to add a lot of value to a service that was working well and make something that works even better in terms of high-performance automation. It showcases what is possible to do with such a system and could push the performance of other beamlines too.\u201d<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>This project was made possible by the synergy between the capabilities of HTX lab and the MASSIF-1 beamline. MASSIF-1 has offered the new CrystalDirect&#x2122; modalities to external academic users since October last year. \u201cIt is quite impressive and fulfilling to see such a project taking shape and to share each step of this experience with great scientists and engineers,\u201d said Rocchio. \u201cNow, we want to give the possibility to perform challenging experiments to the entire community and move to high-throughput while working with multiple projects.\u201d&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>Together with the engineers, technicians and scientists involved in the project, Rocchio is also identifying opportunities for improvement, like automating and streamlining even more processes. They are, for instance, working on improving the washing and supply chain of \u2018pins\u2019 \u2013 the crystal sample holders.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>This is just one of many matters that scientists and engineers are discussing over a cup of coffee at EMBL Grenoble&nbsp; \u2013 just like old times. In Felisaz\u2019s words, \u201cThis is how continuous innovation works; we always have in the back of our minds the search for something better.\u201d&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:acf\/vfwp-card {\"id\":\"block_6453991b31949\",\"name\":\"acf\/vfwp-card\",\"data\":{\"image_source\":\"media_library\",\"_image_source\":\"field_602ba83883d48\",\"image\":\"\",\"_image\":\"field_5ebd3243ee8ec\",\"title\":\"Biology meets engineering at EMBL Hamburg\",\"_title\":\"field_5ebd3243ee989\",\"subheading\":\"\",\"_subheading\":\"field_603b4403d386e\",\"text\":\"EMBL Grenoble isn\u2019t alone in exploring synergies between biologists and engineers. At EMBL Hamburg, structural research relies on cooperation between experts in different disciplines, including those in the Instrumentation Team, which consists of physicists, mechanical and software engineers, and robotics experts. Together, they construct diverse instruments for X-ray-based structural biology tailored to the needs of users. Last year, a new transfer system has joined the MARVIN (MultiAxesRobotic-VersatileINstaller) robot family. The MARVIN system enables the quick and safe handling of fragile crystals, which are used by crystallographers to determine the structure of proteins. The new MARVIN will accompany the CrystalDirect\\u0026#x2122; Harvester, which is already in operation at EMBL Hamburg.\",\"_text\":\"field_5ebd3243eea26\",\"link\":{\"title\":\"\",\"url\":\"https:\/\/www.embl.org\/news\/lab-matters\/biology-meets-engineering\/ \",\"target\":\"\"},\"_link\":\"field_5ebd3243eeac3\",\"style\":\"bordered\",\"_style\":\"field_5ebd3244102b1\",\"image_ratio\":\"default\",\"_image_ratio\":\"field_61d41d4bcbbee\"},\"align\":\"\",\"mode\":\"preview\"} \/-->\n\n<!-- wp:acf\/vfwp-card {\"id\":\"block_645399f43194b\",\"name\":\"acf\/vfwp-card\",\"data\":{\"image_source\":\"media_library\",\"_image_source\":\"field_602ba83883d48\",\"image\":\"\",\"_image\":\"field_5ebd3243ee8ec\",\"title\":\"Funding\",\"_title\":\"field_5ebd3243ee989\",\"subheading\":\"\",\"_subheading\":\"field_603b4403d386e\",\"text\":\"Over the years, the CrystalDirect\\u0026#x2122; project has been, in part, funded by EC infrastructure grants like Bioxhit, iNEXT, iNEXT discovery, as well as by ANR grants and to some limited extent by Instruct-ERIC. This helped fund the construction of the CrystalDirect-2 machine, which is now installed at MASSIF-1. The MASSIF-1 upgrade project is a collaboration between EMBL and ESRF. User access to the new pipelines exploiting the integration of HTX lab services and the new capabilities of CrystalDirect-2 at MASSIF-1 are funded by Instruct-ERIC and the EC-funded iNEXT Discovery, via the HTX lab with beam time provided by the ESRF, as per the EMBL-ESRF agreement.\",\"_text\":\"field_5ebd3243eea26\",\"link\":\"\",\"_link\":\"field_5ebd3243eeac3\",\"style\":\"striped\",\"_style\":\"field_5ebd3244102b1\",\"image_ratio\":\"default\",\"_image_ratio\":\"field_61d41d4bcbbee\"},\"align\":\"\",\"mode\":\"preview\"} \/-->\n\n<!-- wp:acf\/vfwp-card {\"id\":\"block_645399803194a\",\"name\":\"acf\/vfwp-card\",\"data\":{\"image_source\":\"media_library\",\"_image_source\":\"field_602ba83883d48\",\"image\":\"\",\"_image\":\"field_5ebd3243ee8ec\",\"title\":\"Celebrating 100 issues of EMBLetc.\u00a0\",\"_title\":\"field_5ebd3243ee989\",\"subheading\":\"What was it like to work in structural biology back in 1999? \",\"_subheading\":\"field_603b4403d386e\",\"text\":\"\\u003c!\\u002d\\u002d wp:paragraph \\u002d\\u002d\\u003e\\r\\n\\r\\nWe asked Matthew Bowler, beamline scientist co-responsible for the MASSIF-1 beamline.\\r\\n\\r\\n\\u003c!\\u002d\\u002d \/wp:paragraph \\u002d\\u002d\\u003e \\u003c!\\u002d\\u002d wp:paragraph \\u002d\\u002d\\u003e\\r\\n\\r\\nIn 1999, Bowler was a Master\u2019s student working on membrane proteins and had obtained beamtime at a brand new beamline at the ESRF. This beamline had just opened and was run by an EMBL scientist, Andy Thomson \u2013 now working at the SOLEIL synchrotron.\\r\\n\\r\\n\\u003c!\\u002d\\u002d \/wp:paragraph \\u002d\\u002d\\u003e \\u003c!\\u002d\\u002d wp:paragraph \\u002d\\u002d\\u003e\\r\\n\\r\\n\u201cI was incredibly excited to travel from the United Kingdom to Grenoble to use this new beamline. Membrane proteins are very difficult to crystallise and need a lot of screening. We managed to screen 10 crystals in 24 hours. It seemed amazing at that time because you could only get a very limited number of crystals, and you had to do everything manually. But if you compare it with what it\u2019s possible to do today, it\u2019s just completely different! Now you can get through 200 to 500 crystals in a day \u2013 without anyone having to be physically present and manipulate things. \u201d\\r\\n\\r\\n\\u003c!\\u002d\\u002d \/wp:paragraph \\u002d\\u002d\\u003e\",\"_text\":\"field_5ebd3243eea26\",\"link\":\"\",\"_link\":\"field_5ebd3243eeac3\",\"style\":\"bordered\",\"_style\":\"field_5ebd3244102b1\",\"image_ratio\":\"default\",\"_image_ratio\":\"field_61d41d4bcbbee\"},\"align\":\"\",\"mode\":\"preview\"} \/-->","post_title":"Behind the scenes of innovation","post_excerpt":"EMBL Grenoble technology teams provide a sneak peek into their latest collaborative project in structural biology services: the complete automation of an integral step in X-ray crystallography.","post_status":"publish","comment_status":"closed","ping_status":"closed","post_password":"","post_name":"behind-the-scenes-of-innovation","to_ping":"","pinged":"","post_modified":"2025-05-08 11:39:22","post_modified_gmt":"2025-05-08 09:39:22","post_content_filtered":"","post_parent":0,"guid":"https:\/\/www.embl.org\/news\/?post_type=embletc&#038;p=58537","menu_order":0,"post_type":"embletc","post_mime_type":"","comment_count":"0","filter":"raw"},{"ID":58543,"post_author":"124","post_date":"2023-05-15 12:00:00","post_date_gmt":"2023-05-15 10:00:00","post_content":"<!-- wp:paragraph -->\n<p>With the ambitious aim of examining life along European coasts, EMBL\u2019s planetary biology flagship project Traversing European Coastlines (TREC) launched officially in March this year. A press conference in Paris on 8 March 2023 introduced the project to audiences in Europe, along with its aim of studying coastal ecosystems and their response to the environment, on scales from molecules to communities.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59171,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/TREC-1024x614.jpg\" alt=\"Collage of six photographs showing delegates and reporters during a press conference.\" class=\"wp-image-59171\"\/><figcaption class=\"wp-element-caption\">EMBL DG and colleagues during the official launch of TREC in Paris, France. Credit: Mylene Andre\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>The expedition has been several years in the making. The launch of EMBL\u2019s 2022-26 programme unveiled the organisation\u2019s visionary new plan to study \u2018life in context\u2019. To help achieve this, EMBL initiated several transversal themes which support the multidisciplinary science necessary to realise projects like these. One of these themes is Planetary Biology, 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<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>TREC is the Planetary Biology transversal theme\u2019s flagship project, and it aims to explore the interactions within and between the two major ecosystems on our planet: ocean and land. It will bring molecular sciences to environmental research in a Europe-wide project at an unprecedented scale, to better understand how organisms \u2013 from viruses to animals \u2013 respond to natural and human-made environmental changes.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59049,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/ENG-CARTE-TARA-EUROPA-420x297mm-Avec-cartouche-Digital-1024x724.jpg\" alt=\"Map showing all TREC stops and sites..\" class=\"wp-image-59049\"\/><figcaption class=\"wp-element-caption\">Map of proposed TREC sampling sites along the coast of Europe. Credit: Tara Europa.<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>The expedition began in Roscoff, France in April 2023 and will conclude in Malta in mid-2024. During this period, researchers from EMBL, the Tara Oceans consortium, together with the Tara Ocean Foundation, and numerous European collaborating institutes and organisations will work at 120 sampling sites along the European coastline.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>TREC will combine the scientific expertise of many partners as well as existing knowledge of local ecosystems and processes, with EMBL\u2019s latest technology developments and expertise in examining life at the smallest scales.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>The sampling kicked off in Roscoff in April 2023, with researchers from EMBL and Tara, as well as partner institutions including the Station Biologique de Roscoff, heading off to collect soil, water, and sediment samples that will help move forward the expedition\u2019s constituent <a href=\"https:\/\/www.embl.org\/about\/info\/trec\/projects\/\">scientific projects<\/a> and provide a snapshot of the health of these ecosystems.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59167,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/TREC2-1024x614.jpg\" alt=\"Collage of six photographs showing various groups of researchers doing field sampling.  \" class=\"wp-image-59167\"\/><figcaption class=\"wp-element-caption\">Researchers collecting samples at Roscoff, France during April 2023. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>A recurring challenge for molecular biology field expeditions is the lack of ready access to sophisticated lab facilities, which are often needed for sample preparation for advanced applications like electron microscopy. The TREC expedition provides a unique and innovative solution to this \u2013 to bring the labs to the samples rather than the samples to the labs.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>It will achieve this with the help of mobile laboratories, which will travel to specific stops and include cutting-edge light microscopy, sample preparation for (cryo)-electron microscopy, and single-cell pheno-genomics. Additionally, advanced tools for environmental measurements from soil, air, sediment, and water samples will be part of the standard equipment. By providing these technologies across Europe throughout the expedition, EMBL Advanced Mobile Services will support the interdisciplinary approaches that underpin TREC.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59187,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/TREC8-1024x302.jpg\" alt=\"Collage of three photographs showing the interior and exterior of the van that houses the mobile sample processing lab. \" class=\"wp-image-59187\"\/><figcaption class=\"wp-element-caption\">EMBL\u2019s Advanced Mobile Services, including this Sample Processing Lab, will enable scientists to perform leading subcellular research in direct proximity to the field. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:heading -->\n<h2><strong>Engaging with the public in our member states<\/strong><\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph -->\n<p>However, TREC\u2019s aims and scope are not limited to answering scientific questions and bringing state-of-the-art mobile services to European coasts. We live in an interconnected world, and coastal regions are key functional ecosystems on which humans depend for their livelihoods and well-being. Two of the aims of this expedition are also to engage the general public in debate and discussion to raise awareness of the role of science in society and to inspire the next generation of scientists by raising awareness of the importance of understanding life on this planet among pupils and teachers.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>To this end, EMBL\u2019s office of Science Education and Public Engagement (SEPE) is travelling alongside TREC to various coastal sites and conducting public engagement activities aimed at engaging, informing, educating, and entertaining non-expert audiences and spreading awareness regarding the importance of coastal ecosystems.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59173,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/TREC3-1024x614.jpg\" alt=\"Collage of six photographs showing people participating in public engagement activities.\" class=\"wp-image-59173\"\/><figcaption class=\"wp-element-caption\">Caption: Public engagement activities by SEPE at Roscoff, France. Credit: Kinga Lubowiecka\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:heading -->\n<h2><strong>The Road to Roscoff<\/strong><\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph -->\n<p>While TREC officially began in 2023, its organisers have been working tirelessly behind the scenes for many years to plan a successful expedition and smooth out any wrinkles. Three separate pilot expeditions were conducted between 2019 and 2022, helping the researchers optimise the sample collection procedures and associated processes that would serve them in the field during the main expedition, among other things.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:paragraph -->\n<p>The first pilot was conducted <a href=\"https:\/\/www.embl.org\/news\/science\/living-laboratories\/\">in Naples<\/a> and the nearby island of Ischia, where scientists collected samples of microbes and marine organisms at several spots along Ischia\u2019s coast, in collaboration with the Stazione Zoologica Anton Dohrn di Napoli (SZN), a marine research institute in Naples, which also runs a research station on Ischia.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59175,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/TREC4-1024x614.jpg\" alt=\"Collage of six photographs showing a team of researchers collecting field samples.\" class=\"wp-image-59175\"\/><figcaption class=\"wp-element-caption\">Glimpses of sample collection from the coast of Naples during a TREC pilot project in 2019. Credit: Patrick Mueller\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>A second pilot took place in Villefranche-sur-Mer, France in 2021. EMBRC hosted this expedition that enabled unprecedented high-definition ultrastructure images from fresh samples, such as this plankton which was frozen under high pressure on the beach. Soil and sediments were also sampled along the Villefranche sea-land transects and the river Var estuary.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59183,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/TREC7-1024x299.jpg\" alt=\"\" class=\"wp-image-59183\"\/><figcaption class=\"wp-element-caption\">Researchers collecting samples during the TREC pilot expedition in Villefranche-sur-Mer, France in 2021. Credit: Paola Bertucci\/EMBL<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:paragraph -->\n<p>The <a href=\"https:\/\/www.embl.org\/news\/embletc\/issue-99\/from-coast-to-coast-and-beyond\/\">third and final TREC pilot expedition<\/a> was held in Iceland during 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 core TREC expedition in 2023 and 2024.<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:image {\"id\":59179,\"sizeSlug\":\"large\",\"linkDestination\":\"none\"} -->\n<figure class=\"wp-block-image size-large\"><img src=\"https:\/\/www.embl.org\/news\/wp-content\/uploads\/2023\/05\/TREC5-1024x614.jpg\" alt=\"Collage of six images showing researchers collecting and analysing samples, as well as a shot of an erupting volcano.\" class=\"wp-image-59179\"\/><figcaption class=\"wp-element-caption\">EMBL researchers conducted a pilot project in Iceland as the final preparatory step before commencing their journey traversing European coastlines. The visit coincided with a volcanic eruption located 60 Km from the first sampling site. Credits:&nbsp;Niko Leisch\/EMBL, Hiral Shah\/EMBL, Richard Jacoby\/EMBL, \u00a9Kristinn Ingvarsson\/University of Iceland<\/figcaption><\/figure>\n<!-- \/wp:image -->\n\n<!-- wp:heading -->\n<h2><strong>Forging ahead<\/strong><\/h2>\n<!-- \/wp:heading -->\n\n<!-- wp:paragraph -->\n<p>The TREC expedition is the first time researchers from across Europe will study life at all biological scales, from molecules to communities, along the entire European coast, to provide a richer and deeper understanding of how ecosystems respond to natural and human-made challenges. This will produce new knowledge and discoveries that will help to provide our societies, governments, and regulatory agencies with the ability to best predict the possible effects of environmental changes and impacts. It is an ambitious \u2013 and essential \u2013 project,&nbsp;given the environmental challenges that our planet faces.&nbsp;<\/p>\n<!-- \/wp:paragraph -->\n\n<!-- wp:acf\/vfwp-card {\n    \"id\": \"block_645b59a065456\",\n    \"name\": \"acf\\\/vfwp-card\",\n    \"data\": {\n        \"image_source\": \"media_library\",\n        \"_image_source\": \"field_602ba83883d48\",\n        \"image\": \"\",\n        \"_image\": \"field_5ebd3243ee8ec\",\n        \"title\": \"\",\n        \"_title\": \"field_5ebd3243ee989\",\n        \"subheading\": \"Funding\",\n        \"_subheading\": \"field_603b4403d386e\",\n        \"text\": \"<span style=\\\"font-weight: 400;\\\">TREC was made possible with the help of generous support from its member states, as well as many institutions, donors and sponsors, in particular the Manfred Lautenschl\u00e4ger-Foundation, Eppendorf SE, Carl Zeiss Microscopy, and Friends of EMBL.<\\\/span>\",\n        \"_text\": \"field_5ebd3243eea26\",\n        \"link\": \"\",\n        \"_link\": \"field_5ebd3243eeac3\",\n        \"style\": \"striped\",\n        \"_style\": \"field_5ebd3244102b1\",\n        \"image_ratio\": \"default\",\n        \"_image_ratio\": \"field_61d41d4bcbbee\"\n    },\n    \"align\": \"\",\n    \"mode\": \"preview\"\n} \/-->","post_title":"In pictures: the story of TREC","post_excerpt":"EMBL\u2019s newest expedition attempts to answer some of the biggest questions in planetary biology, and will help scientists find solutions to pressing global concerns. 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