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CORBEL News | Issue 9

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NEWS

How CORBEL enables interdisciplinary research in Europe: news from our Open Calls for research projects

The CORBEL 2nd Open Call for research projects, which closed on 31 December 2018, generated a lot of interest among European scientists: 23 project applications from academia and industry covering all of the five offered Access Tracks were received. From all eligible projects, 16 applications were accepted as CORBEL user projects after undergoing a thorough scientific and technical review. The users now have the unparalleled chance to access the requested high-end technologies and services at more than 20 service providers from 10 European biomedical research infrastructures in order to advance their projects.

Most of the user projects took up their work right away as the service provision has to be completed by the end of the CORBEL project in May 2020. All projects will receive continuous support by the CORBEL Open Call project managers during the access phase as needed.

Meanwhile, the CORBEL users from the 1st Open Call continue to benefit from the offered services - read about Camilla Lazzi’s experience below.

Investigating Toxin-Antitoxin systems in lactic acid bacteria

CORBEL user Camilla Lazzi works in the Department of Food and Drug of the University of Parma, Italy as a food microbiologist in the research field of lactic acid bacteria. These are microorganisms with a wide ecological distribution and important applications, especially in the food industry. Their activity as fermentation workhorses is highly regulated. A bacterial community can induce death or dormancy of some cells, in response to different stress conditions, resulting in a sacrifice to favor the survival of the entire ecosystem. These responses are often mediated by a Toxin-Antitoxin (TA) system. TA systems are two-component systems that involve a stable toxin, able to kill the cells or confer growth stasis, and an unstable antitoxin which inhibits toxin activity. Little is known about the distribution and function of TA systems in lactic acid bacteria, but the activation of these systems could modulate the bacterial population dynamics. Understanding the mechanism of action could have promising scientific and applicative perspectives in the field of fermented food but also in the study of intestinal microbiota.

With the use of CORBEL facilities, Camilla and the research group of Parma University aim to identify TA systems in wild isolates of Lactobacillus strains, and subsequently characterize the mode of action of the TA systems. They collaborate with two service providers, the Biomedical Research Foundation of the Academy of Athens (BRFAA) and the Institute of Photonic Sciences (ICFO). The results of the sequencing at BRFAA were presented at the 26th ICFMH Conference FoodMicro2018. Furthermore, a postdoc student, Alessia Levante, plans to visit BRFAA to perform the final elaboration of the data with Dr. Giannis Vatsellas and Dr. Periklis Makrythanasis. As a second step, Camilla and the research group at Parma University want to elucidate the function of the newly identified TAs. To this end, they requested the ICFO in Barcelona as service provider to perform high-resolution fluorescence microscopy (PALM microscopy). Also in this case, a PhD student will spend a period of time at the service provider to set up the final experimental procedure in collaboration with Dr. Pablo Loza, Dr. Maria Marsal and Dr. Jordi Andilla.

'When we read about the CORBEL open call we thought it was a great opportunity to gain access to important Research Infrastructures with experience that is not at all present in our laboratory. Through this call, we have filled a gap improving our research.' - Camilla Lazzi, University of Parma, project leader

Research group of Parma University, Department of Food and Drug (from left to right): Claudia Folli, Stefania Grifone, Korotoum Yabre, Alberto Ferrari, Alessia Levante, Camilla Lazzi (missing: Erasmo Neviani, Barbara Montanini)

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New CORBEL deliverables published

Three CORBEL deliverables were recently published:

 

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Webinar recordings available

Since 2017, CORBEL has been running a webinar series to address challenges and share best practices between the biological and medical European research infrastructures. The series is aimed at technical operators of RIs and is aligned with the CORBEL competency framework. By now, 11 recordings are publicly available on our website, addressing topics such as 'Identifying and Networking with Industry', 'The Access Management Software ARIA', 'Data Sharing and Reuse from Clinical Trials', 'Quality Management in Distributed Research Infrastructures', and 'BBMRI-ERIC Quality Management Services'. Visit our website to learn more!

 

RI in the SPOTLIGHT

This section will focus on one of the thirteen research infrastructures participating in CORBEL, providing useful information for current and future users. In this issue, Instruct-ERIC is introduced to the researcher community.

Instruct-ERIC is a pan-European research infrastructure in structural biology, making high-end technologies and methods available to users from Instruct member countries. Users are given access to highly specialised instruments, with on-site expertise to help them gain the best results for their projects. Structural biology is one of the key frameworks on which we interpret molecular and cellular functions. The main experimental technologies are complementary, and increasingly link detailed atomic structure with cellular context. Structural biology is currently in the middle of a revolution enabled by significant advances in the tools and technologies available (direct electron detectors in EM, advances in synchrotron sources and detectors, XFELs, ultra-high field NMR, super-resolution cryo-light microscopy).

Instruct-ERIC has been proud to facilitate the CORBEL open calls through its ARIA access management software. ARIA is a cloud based suite of services including peer review, visit and remote access management, instrument booking, document hosting, website building tools and more, all with styling to meet specific branding requirements. ARIA is used by many research infrastructures, research projects, and facilities across Europe including iNEXT, EMBRIC, Instruct and Euro-BioImaging. ARIA has been heavily adapted to meet the requirements for combined access to multiple research infrastructures. We have very much enjoyed working on CORBEL open calls, strengthening the partnerships between research infrastructures and enabling interdisciplinary projects. Working together with CORBEL has furthered the development of our software, improving the workflow and adding more configurable options which will make ARIA even better suited to future collaborations between research infrastructures. Together, we have produced training webinars for to the CORBEL open calls for reviewers and for service providers which are available to view online. To find out more about ARIA, visit aria.structuralbiology.eu or contact aria@instruct-eric.eu

 

UPCOMING EVENTS

Data Visualisation for Biology: a practical workshop on design, techniques and tools
March 11-15, 2019 in Hinxton, UK

The EBI training team in association with CORBEL will be running the course "Data Visualisation for Biology: a practical workshop on design, techniques and tools” from 11-15 March 2019 at EMBL-EBI, Hinxton, UK. In this 5-day workshop, we will dive into the topic of biological data visualisation and how it can be used to gain insight in and get a "feel" for a dataset, so that targeted analyses can be defined. This course is targeted at biologists who want to explore, and gain further insight, into their own data through the use of visualisation and design approaches. More information is available here.

European Chemical Biology Symposium (6th ECBS/LS-EuChemS Meeting)
April 3-5, 2019 in Madrid

Chemical biologists from all parts of Europe and overseas come together to present and discuss the latest achievements in cutting edge chemical sciences. This present joint meeting gathers researchers from organic & biological chemistry, proteins biotechnology, computational biology, protocells, machine learning, bacterial resistance, drug discovery, synthetic biology, biomedical materials and chemical glycobiology. The ECBS 2019 is jointly organized by the EuChemS Division “Chemistry in Life Sciences” (LS-EuChemS) and EU-OPENSCREEN ERIC. More information is available on the website.

International Clinical Trials Day (ICTD) 2019
May 20, 2019 in Paris
ECRIN's 2019 celebration of International Clinical Trials Day (ICTD) will take place in Paris, France on May 20, 2019, focusing on challenges raised by patient stratification studies. More information will be available on the ECRIN website soon.

Instruct Biennial Structural Biology Conference 2019
May 22-24, 2019 in Alcalá de Henares, Madrid

The next Instruct Biennial Structural Biology Conference takes place May 22-24, 2019 in Alcalá de Henares, Madrid, Spain, under the topic "Structural Biology: Deeper into the Cell". Registration is open until 1 April 2019, the abstract submission deadline is 1 March 2019. More information is available on the conference website.

 

MEET US @

 

REPORTS

Staff Exchange 'INSTRUCT ARIA introduction and adaptations for EU-OPENSCREEN ERIC'

In the CORBEL Project, transnational user access projects are implemented using the user-friendly online access management system ('ARIA'), which was developed by INSTRUCT ERIC. This system covers all administrative stages of the project including proposal submission, review, and project execution and reporting. To learn more about how this administration system for the management and tracking of user projects can be customised to the needs of EU-OPENSCREEN ERIC, Katja Herzog visited the INSTRUCT central office from 14-17 August 2018 in Oxford (England). Katja got insights into all identifications, functionalities and feasible customisations in ARIA concerning proposal workflows, centre and technology configurations, access routes, forms, calls and surveys, management of administration and finances, possibility of a content-management system, booking calendar and network options. In a second step, Katja directly tested general features in the beta version of the ARIA system. Together with the INSTRUCT team, Katja discussed the development of potential future features and the next steps for the implementation of ARIA for EU-OPENSCREEN.

'In addition to learning how to further streamline our project management and administrative workflows with ARIA, it was extremely helpful to get insights into the daily operations (legal/ financial/ outreach) of the INSTRUCT central office and to discuss administrative hurdles linked to the establishment of ERICs. Many thanks to the INSTRUCT team for this very insightful and well-prepared staff exchange as well as the very warm welcome.' - Katja Herzog, EU-OPENSCREEN ERIC

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CORBEL MIUF Meeting

The CORBEL Medical Infrastructure/ Users Forum (MIUF, WP3.1) held its third annual meeting in Paris on 15 October 2018.

The MIUF is designed to promote close collaboration, at the pan-EU level, between medical research communities, funding bodies, and medical RIs. In particular, its mission consists of promoting the establishment of pan-European scientific communities, providing the scientific content and access to patients; clearly defining the respective roles of infrastructures vs. scientific communities, avoiding gaps, overlaps and fragmentation; capturing the needs of the scientific communities and of the funders in terms of infrastructure services; and of ensuring the appropriate development and deployment of these services by one or multiple research infrastructures.

The October 2018 MIUF meeting was intended to discuss

  • the structuring of medical research communities at the pan-European level
  • the emerging needs of medical research projects in the context of the big data and personalised / stratified medicine approach
  • and the challenges raised in terms of development and deployment of data services

The session on medical community structuring provided an overview of many recently-funded European initiatives on: infectious diseases (ECRAID), neurosciences (EBRA), vaccines (TRANSVAC-2), paediatrics (IMI C4C) and rare diseases (EPJ-RD). Some of the challenges noted included: project sustainability, quality control, education/training (e.g. in vaccinology), information sharing and strategic vision.
The session on new research models highlighted various ‘success stories’ in the context of the new medical research paradigm in Europe. The potential value of cross-cutting collaboration between academia and industry was underlined in a case study on EATRIS/NeurATRIS. In particular, the challenges for image analysis/machine learning were noted (e.g. data collection, anonymization, clean-up/structuring, storage, sharing, inspection/annotation, processing/analysis, integration).
The session on personalised medicine and patient stratification focused on developments in today's research landscape: multimodal data management and machine learning processing. Speakers highlighted various issues such as the storage and sharing of data, and the optimisation of research to avoid lengthy (useless) trials.
The final session continued the discussion on data challenges, with speakers detailing issues from the organisation/sorting of data to determining which repository to use.

 

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3rd CORBEL Annual General Meeting

The CORBEL consortium met from 16-17 October 2018 for its 3rd Annual General Meeting, organised in Paris by ECRIN-ERIC. During the meeting, all work packages reported on their recent achievements and discussed next action steps in several plenary and parallel sessions. In a flash talk session, a number of other European projects involving the biomedical research infrastructures were presented. Moreover, the assembly offered the opportunity for meetings of the CORBEL Executive and e-Infrastructure Advisory Boards as well as the BMS RI Strategy Board. Due to the extension of CORBEL until the end of May 2020, the final CORBEL General Assembly will be held in spring 2020.

 

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CORBEL @ ELIXIR Innovation Forum and ENABLE Conference

In order to reach out to potential users of research infrastructure resources, CORBEL was present for two events at the end of 2018: the ELIXIR Innovation and SME Forum on 'Data Driven Innovation in Industrial Biotechnology', which took place in Frankfurt/Main, Germany, from 15-16 October 2018, and the ENABLE (European Academy for Biomedical Science) initiative's 2nd European PhD and Postdoc symposium on 'The Promise of Future Medicine: From Research to Therapy', held in Copenhagen from 7-9 November 2018.

The events provided many opportunities to interact and network, both with researchers from industry as well as with early-career scientists from the biomedical field. The CORBEL 2nd Open Call was presented on both occasions, and information about the biomedical research infrastructures and CORBEL in general was given.

 

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EATRIS hosts successful training workshop on academia-industry collaborations

The European Research Infrastructure for Translational Medicine (EATRIS), leader of the CORBEL WP8 'Accelerating Innovation', organised a training workshop 'Best Practices in Biomedical Public-Private Research Collaborations: Network Development, Legal Planning & Project Management' in Ljubljana, Slovenia, from 12-13 December 2018.

The workshop aimed to offer practical tools and insights to academic groups as well as to staff from biological and medical research infrastructures (RIs) to accelerate their partnerships with industry and the innovation potential of their RI. The two-day training covered the many aspects of setting up public-private collaborations (business development strategy, legal frameworks, project management); it was followed by an interactive group exercise featuring a realistic case study. The programme and exercise were based on the perspective of the academic researcher, who is required to take an active role in setting up public-private collaborations. EATRIS and other biomedical infrastructures were invited to give highlights from their experience in reaching out to industry, and a pharmaceutical consultant gave a talk on the industry point of view.

Judging by the high level of enthusiasm and the positive comments received, the workshop fulfils a clear need in academia. We hope to repeat the workshop during the remainder of the CORBEL project. For more information on this workshop and innovation-related activities under CORBEL, please visit the EATRIS website or contact: nigelwagstaff@eatris.eu

 

UPDATES FROM PARTNERS

On 29 November 2018, the Portuguese representation has submitted the files for the first step submission of MIRRI-ERIC to the European Commission. Eight countries have signed the Memorandum of Understanding for MIRRI: Belgium, France, Greece, Latvia, the Netherlands, Spain, Poland and Portugal. Other countries demonstrating interest include Italy, Romania, and Russia.

The 4th Instruct Biennial Structural Biology Conference 2019 will be taking place in Alcalá de Henares, Spain from the 22 to 25 May 2019. We have an exciting lineup of speakers and sessions covering topics from "Structural biology towards cellular biology" to "Emerging technologies in integrative structural biology”. Registration is open here and user abstract submissions are invited here. Eligible abstracts will be selected for poster presentation and four abstracts will be selected for oral presentation at the conference. The deadline for abstract submission is March 1st, and the deadline for registration is April 1st. Student fellowships are also available, see here for details.

RI-VIS is a new H2020 project, starting on the 1st of February 2019, working to increase the visibility of European Research Infrastructures, forging new strategic partnerships and reaching out to new broader audiences including those in target regions worldwide. The project consortium is composed of 13 partners spanning 12 infrastructures in the biomedical, social, and environmental sciences. We are looking forward to making new connections and spreading the word about the fantastic opportunities available through European Research Infrastructures. Follow us on Twitter @RI_VIS_eu.

New contact data for EU-OPENSCREEN: Please visit our coordination team website for changed EU-OPENSCREEN ERIC staff contact data, as EU-OPENSCREEN is now an independent ERIC

New team member at EU-OPENSCREEN: Tanja Miletic, Ph.D., joined the EU-OPENSCREEN ERIC team on January 1st, 2019. As a Grant and Project Manager, Tanja will mainly work on CORBEL and other H2020 grants. She studied organic chemistry and worked on the design and synthesis of novel functional chromophores for light harvesting applications (University of Trieste) as well as the preparation and characterisation of novel functional materials based on heteroatom doped polycyclic aromatic hydrocarbons (Cardiff University) before joining EU-OPENSCREEN ERIC.

New H2020 projects: EU-OPENSCREEN ERIC coordinates the H2020-INFRADEV-2018-1 EU-OPENSCREEN-DRIVE project (starting February 1st) and participates as a partner in the following new H2020 projects: H2020-INFRASUPP-2018-1 Ri-Vis, H2020-INFRASUPP-2018-1 ERIC-Forum, H2020-INFRAEOSC-2018-2 EOSC-Life

MERIL has launched the Advanced Data Module. With this third and final data module, MERIL paves the way for its final data collection efforts. RI coordinators can provide information for 21 data fields related to their research infrastructure’s impact, funding and HR. The collected data portrays the active use of research infrastructures and metrics on RI outputs, which are relevant for European policy makers. This will foster engagement and help demonstrate an RI’s positioning within the European RI landscape. RI coordinators who have already published entries are encouraged to return to the MERIL portal to edit their existing page. The module for Advanced Data can be found at the bottom of their RI profile page.

EMBRIC is organizing a European Parliament facing workshop, symposium and roundtable showcasing European research in "Mining for Valuable Bioactive and Enzymes from Marine Algae and Bacteria" on 5 March 2019 in Brussels, Belgium. The workshop will welcome a range of experts from academia and industry who will discuss steps to unlock the vast potential for this research to positively impact health, society and the economy. Registration is open - more information and the registration link is available here.

EMBRIC has set up a survey to find out how investors/company owners and policy makers view the Blue/Marine Bioeconomy. We would like to learn which resources are in the focus, how you perceive the market situation and where you see challenges/opportunities. The insights collected will feed into a roadmap that will be developed as a legacy of EMBRIC. It will be a contribution to the discussion at EU level on the future development of the blue bioeconomy and reinforce the communication between the marine Research Infrastructures, biotech companies and policy makers. Completing the survey takes around 2 minutes – we would be grateful for your input!

 

PUBLICATIONS

Sharing individual participant data from clinical studies: a cross-sectional online survey among Italian patient and citizen groups (2019) Colombo, C., Anna Roberto, A., Krleza-Jeric, K., Parmelli, E., Banzi, R., BMJ Open, DOI: 10.1136/bmjopen-2018-024863

This project receives funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No 654248.

This publication reflects the view only of the author(s), and the European Union cannot be held responsible for any use which may be made of the information contained therein.

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