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Creative teamwork leads DigiBio project to success in its first year
The first year of the DigiBio project has passed and we can safely call it a success. It has been a creative, interesting, and hard-working year full of new ideas, surprises, and great collaborations. Our project partners from Denmark (Novo Nordisk Foundation Centre for Biosustainability) and TalTech are increasingly engaging with this challenging team effort.
This year can be considered a foundational stage, while the next will be a stage of accelerated influx of scientific data and synthesis of knowledge facilitated by our fully automated digital Biofoundry. We have renovated the labs and offices for the Biofoundry and Digi units in Chemicum, the building next to our current institute. This will become our temporary space until the new laboratory and study building, Logicum, is built and move-in ready by 2029.
We are currently procuring the Biofoundry equipment and designing the workflow details. It is a highly complex effort, like building and optimizing a small high-tech factory. We have hired the Director of the Biofoundry, Dr Vallo Varik from EMBL, Heidelberg, and the Leader of the Sustainable Innovation Office, Dr Rainis Venta. The staff of the Biofoundry and Digi units have almost been fully recruited.
To gain full autonomy – a central requirement of the Teaming programme – we have established the brand-new Institute of Bioengineering as an upgrade to the Centre of Synthetic Biology, which was founded in 2016. We began this year with four research groups and will have six at the beginning of 2025. The goal of the Institute is to grow to 12-14 research groups by the time we move to the new building in 2029.
Project acquisition and financial sustainability are two of the main goals of the Teaming projects since the initial investment of 30 million euros is only seed money. We have made terrific progress towards these goals during the first year of the project (see the Scheme).
The year opened with wonderful news. Professor Kaspar Valgepea won the most prestigious of all research grants: an award from the European Research Council (ERC CoG ERC, 2.5 million euros for the synthetic biology of gas fermenting bacteria to improve carbon capture and sustainable chemical production). We are also excited about the TreeBioTEC ERA Chair, a 2.5 mEUR project to develop the bioengineering of birch trees and recruit a world-famous expert in tree bioengineering from Finland.
In addition, we received three applied science projects (totalling 3.5 million euros) that are very well suited for implementation within Biofoundry workflows. On top of two personal research grants, basic science and teaching funds, and a few smaller EU and other international projects, we raised ca 13 million euros in additional funds during the first year to ensure the sustainability of DigiBio and the Institute of Bioengineering. By the start of the next year, we will have six research groups involving three ERC grant holders or ERC alumni. We intend to keep the ERC success rate – the main excellence criteria of scientific institutions in Europe – at 50%, matching the best research centres in Europe and presenting a leading example for other institutes in Estonia.
Furthermore, as a result of the Erasmus Mundus collaboration with esteemed universities such as Heidelberg, Groningen, and Uppsala, we will establish a brand-new master’s program. This initiative will attract talented individuals who can contribute significantly to DigiBio. Professor Ilona Faustova leads this effort with great enthusiasm and dedication as coordinator of the Estonian team.
Finally, the new institute has been featured on three individual infrastructure roadmaps, which will yield more equipment funds in the future (molecular and cell biology, wood valorisation, plant biology).
The DigiBio project has garnered substantial attention, positioning us as a beacon of hope for local science. Our selection by the Estonian Science Agency to represent the country in Japan at the inaugural event of the forthcoming Estonian-Japanese science collaboration programme best illustrates our recent visibility. Fun, important, and rewarding teamwork characterise this past year. Thank you to our partners at the European Commission who have guided us so thoughtfully through the first steps on this long journey. Special thanks go to our partners in Denmark and Tallinn and the wonderful people on the DigiBio team – Ilona Faustova, Anneli Schön, Jochen Förster, Lars Nielsen, Birte Kastrup Rasmussen, Ervin Valk, Vallo Varik, Hannes Kollist, Andres Merits, Eva Zusinaite, Rainis Venta, Kaspar Valgepea, Kaisa Orgusaar, Eve-Ly Oajngu, Tiit Lukk, Petri-Jaan Lahtvee, and many others.
Opening event for excellence project teaming in digitalised bioengineering and personalised medicine
The official opening event of the teaming for excellence projects in digitalised bioengineering and personalised medicine was held at the university’s main building on 11 September 2023. The event featured speeches from representatives of the European Commission and the Estonian Ministry of Education and Research. University of Tartu researchers and collaborators from international partner institutions also discussed the detailed work plans of the consortia.
At the start of 2023, international consortia led by University of Tartu researchers secured a combined €60 million in funding from the European Commission and the Estonian government. This funding will support the development of two research centres in Estonia over the next six years. Additionally, these centres will play a pivotal role in advancing the digitalized bioindustry and fostering start-ups engaged in data-driven healthcare services.
These initiatives are financially supported through the Teaming for Excellence funding initiative under Horizon Europe, the European Commission’s framework programme for research and innovation. This programme is designed to facilitate collaborative projects among European research institutions, with the goal of conducting cutting-edge research and enhancing its integration into both society and the economy.
Watch the recording of this event here: https://www.uttv.ee/naita?id=34704
UT team Estonia-TUIT wins Grand Prize at world’s largest synthetic biology competition iGEM
Students from the University of Tartu Science and Technology and Bioengineering programmes won the grand prize at the iGEM competition—the largest synthetic biology competition in the world.
Under the guidance of Ilona Faustova, Associate Professor of Molecular Biology, the students engineered yeast to generate small interfering RNA molecules. These molecules are designed to prevent a virus’s genes from being expressed in bee cells. Bees can be protected by consuming the modified yeast or through direct injection into honeycombs. This method not only offers a potential lifeline for bees but also demonstrates a versatile strategy that could be adapted to address other viral infections.
The success of the Estonia-TUIT team at iGEM, which celebrated its 20th anniversary in 2023 with 404 teams from 66 countries and regions, highlights the exceptional talent and innovation within the University of Tartu’s synthetic biology research and education areas. The victory, along with awards for the best conservation project, the best measurement, and a gold medal, highlights the global recognition of Estonian research in this field. Participation in iGEM has been an integral part of the Science & Technology programme’s engagement with synthetic biology, supported by Professor Mart Loog’s laboratory. This achievement demonstrates the potential of dedicated students and the impact of collaborative scientific effort.
Read more here: https://tuit.ut.ee/en/content/university-tartu-students-won-grand-prize-global-synthetic-biology-competition
Institute of Bioengineering launches at UT
The 1st of January 2024 marked a new age in biotech development in Estonia – the newly formed Institute of Bioengineering opened its doors. Professor Mart Loog has been appointed Director of the Institute, with Associate Professor Ilona Faustova serving as Vice Director.
“This new institute is shifting the paradigm in biological studies in Estonia,” says Loog. “Research in molecular biology and genetics has been ongoing in Estonia since the 1960s. The goal of the new institute is to use bioengineering and synthetic biology tools to design, build, and test organisms with desired functions, in other words – to program living cells.”
The institute belongs to the field of natural and exact sciences and its premises are located in Chemicum (Ravila 14a) and at the Nooruse 1 study building. The Institute of Bioengineering was created with the support of the European Commission and the Estonian state as part of the ‘Teaming for Excellence’ measure to implement the DigiBio project, develop bioengineering, and enhance knowledge sharing.
“Thanks to the DigiBio project, a sustainable and state-of-the-art research centre can be developed with the support of the institute as well as its new units, laboratories, and partnerships,” adds Loog. “At the core of the institute’s work is the genetic design of cells used in biotechnology and their construction and application.”
A bioengineering experimental platform for collecting big data, bioengineering digitization units, and a technology transfer unit will be established at the institute. The working groups of Mart Loog, Professor of Molecular Systems Biology; Andres Merits, Professor of Applied Virology; Hannes Kollist, Professor of Molecular Plant Biology; and Kaspar Valgepea, Associate Professor of Gas Fermentation, alongside their employees and students, will transfer from the Institute of Technology to the Institute of Bioengineering.
The institute will teach the English-language bachelor’s programme in Science and Technology led by Ilona Faustova, Associate Professor of Molecular Biology, and the master’s programme in Bioengineering will be coordinated with the Institute of Technology. Among the doctoral students and junior researchers of the Institute of Technology, those whose main supervisor is part of the Institute of Bioengineering as of 1 January 2024 will join the institute.
The partners of the Institute of Bioengineering are the Centre for Biological Sustainability of the Novo Nordisk Foundation of the Technical University of Denmark and the bioengineering laboratories of Tallinn University of Technology.
Kaspar Valgepea receives ERC grant to study gas fermentation
With the support of a 2.3-million-euro grant from the European Research Council, Kaspar Valgepea, Professor of Gas Fermentation Technologies at the University of Tartu, will expand the understanding of the bacteria that consume exhaust gasses. He plans to create a new method for the genetic modification of a large number of bacterial strains and put together a field-supporting body of knowledge. “The new platform for high-throughput microbial genetic engineering will significantly advance the capacities of microbial bioengineering at the Institute of Bioengineering, especially regarding non-conventional organisms,” says Valgepea.
University of Tartu and Tallinn University of Technology sign agreement to establish Estonian Biofoundry
As part of the DigiBio project action plan, the University of Tartu and Tallinn University of Technology signed a partnership agreement on 7 March this year to execute the project’s aims. They will develop the laboratory research infrastructure complex and the bioengineering platform – the Estonian Biofoundry. The joint centre will be managed by the University of Tartu; to support these activities, the Institute of Bioengineering has been established.
The Estonian Biofoundry is an upgrade, catalysed by the DigiBio project, of the Estonian Bioengineering Centre (originally called the Estonian Centre for Synthetic Biology), which was established at the University of Tartu in 2016 within the framework of the European Commission-funded ERA Chair project SynBioTEC and was further developed with the help of the ERA Chair project GasFermTEC. The DigiBio project is funded under the EC Widespread for Excellence Teaming programme with 15 million euros and co-funded by the Estonian state with a further 15 million euros.
The Novo Nordisk Foundation Centre for Biosustainability (DTU Biosustain), a unit of the Technical University of Denmark, will also be involved in managing the centre created at the DigiBio project stage and based on the consortium agreement concluded within it.
One of the most important goals of the cooperation is to act based on the experience of our Danish partner, DTU Biosustain, to combine digital and automated experimental tools for various bioengineering solutions and to find financial and other resources to modernize and ensure the sustainability of the bioengineering platform, including the opportunities offered by the Global Biofoundry Alliance.
Lab space for Biofoundry and offices for Digital Bioengineering platform units renovated
This summer, we renovated the laboratory space for the Biofoundry and supporting equipment rooms as well as a large office space and multiple smaller offices for the units of the Digital Bioengineering platform, the staff of the Sustainable Innovation Office, and the team who will kick-start the Bioeconomy Development Foundation. The equipment procurements for scientific instruments and lab furniture are underway, and the Biofoundry will be functional by late winter this year. This will become our temporary space until the new laboratory and study building, Logicum, is built and move-in ready by 2029.
Institute of Bioengineering awarded Erasmus Mundus grant for international master’s programme Innovative Medicine in collaboration with Uppsala, Gröningen, and Heidelberg universities
Associate Professor Ilona Faustova is leading our University ‘s partnership effort for a new international master’s programme in Innovative Medicine (IMIM) will be a big advantage for developing skills in the field and attracting future talent to Tartu, enabling novel scientific and teaching partnerships and collaborations. The courses and modules teach students how to evaluate and improve current technologies and launch start-ups. To achieve this, students receive training in renowned medical and technological innovation centres in Europe, hands-on experience in several research fields, and training in various aspects such as basic science, clinical research, entrepreneurship, market knowledge, clinical innovation, and societal impact.
As the IMIM’s full partner, the Institute of Bioengineering is launching a new master’s study programme. As a hub for the digitalization of bioengineering and incorporation of AI technologies into cell biology, synthetic biology, gas fermentation technologies, and virology, we will offer students unique opportunities to transition from proof-of-concept to prototype in a shorter timeframe than previous standards allowed. This will facilitate the acquisition of interdisciplinary skills and provide extensive practical laboratory experience.
Upon completion of the programme, students are awarded a Double Degree, with graduates making excellent candidates for both PhD and private sector positions.
Importantly, the new programme aligns with DigiBio’s post-project long-term sustainability goals as it prepares a new generation of researchers for the Institute of Bioengineering and regional biotech.
Vallo Varik joins DigiBio team as Director of Estonian Biofoundry
Vallo Varik has joined the Estonian Biofoundry team within DigiBio to drive innovation. Following his postdoctoral research in systems microbiology at the Nassos Typas lab at EMBL Heidelberg, where he focused on high-throughput approaches to discover and characterize novel antibacterial treatments, Varik is eager to advance data-driven approaches in synthetic biology.
He was drawn to the Institute of Bioengineering’s newly established team because of its emphasis on lab automation, cutting-edge data science, and potential to become a leading centre for groundbreaking biological research and development. Varik is excited to leverage his experience with high-throughput approaches to advance drug discovery and engineer designer cells for next-generation biosustainable solutions. He sees the Estonian Biofoundry as a unique opportunity to introduce novel infrastructure for Estonian life scientists and build international partnerships.
Professor Jochen Förster, CTO of Novo Nordisk Foundation Centre for Biosustainability, welcomed to management board
Professor Jochen Förster joins the management board of the DigiBio project. Jochen is the CTO of DTU Biosustain and Head of the DTU Biosustain Biofoundry.
In March, Professors Mart Loog and Ilona Faustova travelled to Copenhagen. They met with Jochen, Scientific Director Professor Lars Nielsen and other DigiBio project partners from the Technical University of Denmark (DTU) and the Biofoundry. During very productive meetings, the partners shared their experiences, how they established the Biofoundry in Copenhagen, what obstacles they faced, and how this valuable knowledge could be transferred to the Tartu Biofoundry.
We made a general plan and blueprint for the training topics as well as time schedules for researcher and student exchange for the Estonian partners who will visit the Biofoundry and digital bioengineering and data management units in Copenhagen.
Jochen is an expert in developing production strains in a Biofoundry and Pilot Plant. Currently, DTU Biosustain’s Biofoundry is a data-driven technology platform that enables rapid cell factory design for chemical and protein production. It has been established based on a Design-Build-Test-Learn cycle and comprises eight technology teams.
Data analysis is a unique element of the Biofoundry. The Design and Learn teams of the Biofoundry develop and use multiple tools and interoperable databases to transform data into biological meaning, while the Build and Test teams deliver the next efficient cell factory using automation, synthetic biology, adaptive laboratory evolution, and physiological characterization.
The Biofoundry is an integral part of the operations at DTU Biosustain. While the Biofoundry supports all the research groups of the Centre, its overall aim is to bridge the technological ‘valley of death’ and advance selected research projects in developing cell factories for chemical or protein production. Subsequently, these projects can be handed over to the Pre-Pilot Plant for process optimization, scale-up, and the final spin-out or licensing package. To ensure that projects are economically feasible and can have a significant impact on biosustainability, the Biofoundry maintains strong interactions with the Informatics Platform, the Sustainable Innovation Office, and the Commercialization/IP Support team at DTU Biosustain.
Rainis Venta joins Institute of Bioengineering as Innovation Manager
The Institute of Bioengineering at the University of Tartu is thrilled to welcome Rainis Venta as our Innovation Manager, effective 1 August. Rainis’s arrival signals an exciting milestone as we continue to push the boundaries of cutting-edge research and enhance our translational capabilities.
With a diverse background spanning industry-academia collaboration, R&D-intensive start-ups, deep-tech investments, and technology transfer, Rainis brings a wealth of expertise. His strong track record of facilitating technology transfer in high-value manufacturing and bridging multiple ecosystem players—from start-ups to large industries—makes him a vital asset to our team.
Rainis’s appointment is particularly timely as the Institute launches its Sustainable Innovation Office and talent network, designed to unlock radical innovation in areas such as biosustainability, drug discovery, vaccines, and gene therapies.
“My journey has shown me that successful innovation isn’t always about funding or team size, but rather the mindset within an organization,” shares Rainis. “The Institute of Bioengineering’s prepared mindset and entrepreneurial spirit, combined with its top-tier research capabilities, is the perfect recipe for groundbreaking outcomes.”
His arrival also coincides with the Institute’s expansion of the Estonian Biofoundry and the development of modern frameworks for technology transfer to accelerate translational research. Rainis’s leadership will generate a significant translational impact, giving groundbreaking research real-world applications that benefit both industry and society.
Rainis recommends the book The Venture Mindset: How to Make Smarter Bets and Achieve Extraordinary Growth by Ilya Strebulaev and Alex Dang as it has greatly influenced his approach to driving innovation.
Mart Loog, Ilona Faustova, and Kaspar Valgepea participate in Global Biofoundry Alliance (GBA) meeting in Copenhagen
Mart Loog, Ilona Faustova, and Kaspar Valgepea took part in the Global Biofoundry Alliance (GBA) meeting in Copenhagen on 7-8 September 2023. It was the first GBA meeting in which the representatives of the DigiBio project and the newly founded Estonian Biofoundry participated.
Professor Loog delivered a talk introducing the concept and plans for the Estonian Biofoundry and how it can contribute to the GBA and Biofoundry development in the region.
Many important contacts were made during the event. Particularly important was learning about the experiences of others in setting up a biofoundry. These interactions will facilitate the more efficient design and the smoother start-up of the Biofoundry in Tartu.
Ilona Faustova participates in second European Teaming Conference hosted by InnoRenew CoE
Ilona Faustova represented the DigiBio teaming project during the second European Teaming Conference, hosted by InnoRenew CoE. The conference brought together representatives from all 45 active Teaming projects. The primary objective of the conference was to promote the exchange of knowledge, cultivate sustainable networks, and enhance communication with the European Commission.
During the event, European Commission representatives underscored their commitment to project sustainability through periodic reporting and introduced innovative instruments designed to bolster Teaming projects.
The conference showcased panels where seasoned partners openly discussed their experiences in recruiting and retaining highly skilled researchers. Specialized sessions delved into the pivotal role of Centres of Excellence within the European research landscape. Parallel sessions offered participants the opportunity to collaborate based on their project’s specific focus, spanning diverse fields such as materials, physics, digital technology, biotech, agriculture, health, environment, culture, and education.
Additionally, participants visited InnoRenew CoE’s cutting-edge research laboratories. The conference culminated in a special ceremony commemorating the successful conclusion of the InnoRenew project.
Prof Mart Loog gives talk at Cold Spring Harbor Asia meeting ‘Yeast and Life Sciences’ in Japan.
Professor Mart Loog shared our latest scientific work at the Cold Spring Harbor Asia meeting ‘Yeast and Life Sciences’ in Matsue, Japan. Our years-long effort to dissect the main components of yeast pheromone signalling has finally revealed an intricate modular toolbox that can be used to design artificial networks and switches in cells. These findings have the potential to find wide commercial applications in industrial biotechnology and biomedicine in the future.
The Cold Spring Harbor Asia meeting is the Asian branch of the historical Cold Spring Harbor meetings, which were held for decades at the Long Island Cold Spring Harbor Laboratories (CSHL). These prestigious meetings and the CSHL have witnessed the most important developments in the history of molecular biology over many decades.
Forthcoming events in October: focus on scientific collaboration with Asian countries
The DigiBio project team will represent the country at the inaugural event of the Estonian-Japanese science collaboration programme in Tokyo, organized by the Estonian Science Agency. The central topic of the event is ‘Fostering Japanese-Estonian research cooperation in the field of bioengineering and biotechnology’.
The core group from the DigiBio team and the professors of the Institute of Bioengineering – Ilona Faustova, Kaspar Valgepea, Andres Merits, Hannes Kollist, and Mart Loog – will take part in the event as presenters or panellists. The event will be very well attended by the academic elite. Among the delegation travelling to Japan with us are Dr Anu Noorma, Director General of the Estonian Research Council, Prof Toomas Asser, Rector of the University of Tartu, and Prof Tiit Land, Rector of the Tallinn University of Technology. The meeting will be facilitated by Hon. Mait Martinson, Ambassador of Estonia to Japan.
21st annual Science and Technology in Society (STS) forum meeting in Kyoto
Before the event in Tokyo, Prof Toomas Asser, Rector of the University of Tartu, and the DigiBio management team, Professors Ilona Faustova and Mart Loog, will take part in the STS annual forum in Kyoto.
The STS is a society dedicated to matters associated with the advancement of science and technology and how this process raises important ethical, safety, and environmental issues, e.g. possible negative applications are threatening humankind’s future. The forum aims to provide a new mechanism for open discussions on an informal basis and to build a human network that can, in time, resolve the new types of problems stemming from the application of science and technology. The forum community will also explore the opportunities arising from science and technology and address how to remove the barriers to using science and technology to solve the problems facing humankind.
Annual Global Biofoundry Alliance Meeting 2024
Director of the Estonian Biofoundry Dr Vallo Varik will participate in the Annual Global Biofoundry Alliance Meeting 2024 (GBA2024) from 10-11 October at the Daejeon Convention Centre (DCC) in the Republic of Korea. The Global Biofoundry Alliance (GBA) enables the collective to share experiences and resources and work together to overcome shared challenges and unmet scientific and bioengineering needs:
- Develop, promote, and support non-commercial biofoundries established around the world
- Intensify collaboration and communication among biofoundries
- Collectively develop responses to technological, operational, and other common challenges
- Enhance the visibility, impact, and sustainability of non-commercial biofoundries
- Explore globally relevant and societally impactful Grand Challenge collaborative projects
Follow our activities at www.digibio.ut.ee.