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BioEng Lab & ÄIO International Picnic

Before the academic year begins and summer loses its warmth, the BioEng Lab and ÄIO teams decided to have a common lunch in the format of an international picnic. Everyone was invited to bring something representing their country’s cuisine or culture. The table soon filled up with a variety of savoury dishes, sweet cakes and snacks, offering plenty of opportunities to discover something new. 

The biggest surprise of the event, however, was the grill that appeared from the ÄIO’s storage room. Soon, the smell of meat in a Brazilian marinade was filling the Tehnopol air, making it rather difficult to remember that this was supposed to be just a lunch break. 

Instead, it turned into a relaxed afternoon with good food, conversations and plenty of fun — a simple reminder that collaboration can also happen away from desks, meetings and laboratories. 

The same activity next year? 

EventPeople
Summer Day 2026

What´s the better way to enjoy Estonia’s beautiful nature than to escape to one of its islands for a day? This year, the BioEng team decided to explore Aegna island — a place that might surprise you with one interesting fact: although it feels like a remote island getaway, Aegna is actually part of the city of Tallinn! 

Our adventure began on the 17th of July at Tallinn’s Linnahall harbor, where we boarded the ferry. The ferry, which can accommodate around 100 passengers, was packed, with every ticket sold. Most of the passengers were Estonians, which seemed to be a great example of how popular domestic tourism is among locals. 

On the island, our guide was waiting to welcome us, and our adventure began. Our first stops took us into the island’s fascinating history. We explored several places, including the Officers’ Casino and the remains of Peter the Great’s Naval Fortress — more specifically, the “Heavy Batteries of the Tallinn–Porkkala Line”. Walking among these remnants of the past, it was easy to imagine how strategically important this seemingly peaceful island once was. 

After exploring the historical sites, we made our way towards the beach. We found a perfect spot in the shade of the trees and settled down for a picnic. Some brave members of the team dipped their toes into the sea, but despite it being summer, the water was surprisingly ice-cold! 

With renewed energy after lunch, we headed towards one of Aegna’s most mysterious attractions — its magical stone labyrinth. The 11-turn stone labyrinth, also known as “Jerusalem”, is an important part of Aegna’s cultural heritage. Throughout history, labyrinths have been associated with rituals, mystery, and spiritual journeys. This one is said to have been regarded as a ritual sanctuary and a place for connecting with supernatural forces. One of the BioEng members even completed the entire labyrinth — but whether it really has a magical effect remains a secret. 

Our next destination was the impressive Tulekivi boulder. In the past, a fire was lit on top of it to serve as a navigational signal for ships approaching the island. On this day, however, the boulder had a different purpose — it was conquered by the BioEng team! The climb up was surprisingly easy, although getting back down proved to be a little more complicated. 

Our adventure continued with a visit to a boulder field before we followed a magical trail marked by a continuous line of stones. Here, we discovered another fascinating island tradition: everyone who walks the trail is encouraged to pick up a stone from the shore and add it to the markings along the path, making the trail a little longer for the next visitors. In this way, every person who visits becomes a small part of the island’s story. 

Eventually, following the trail, we made our way back to the port. Before boarding the ferry, there was, of course, one final and essential stop: the ice-cream kiosk! As the ferry carried us back towards Tallinn, we could look back on a day filled with sunshine, history, nature, adventure and plenty of laughter. But the day was not over yet. Back in Tallinn, we continued our summer adventure with a delicious Georgian meal. 

And so, with tired legs, happy faces and plenty of new memories, we brought our amazing BioEng Summer Day to an end.

 

(Thank you Adventurehiking OÜ for an amazing guide Jaan Jalas)

NetworkingPeopleProjects
Mid-term Meeting and Workshop by YAF (Yeast-based Solutions for Sustainable Aviation Fuels)

Abdullah Nasir, Subhasis Behera and Laura de Freitas Naves from our BioEng research group recently participated in the two events by YAF (Yeast-based Solutions for Sustainable Aviation Fuels) project.

Mid-term Meeting 

Meeting held at CIEMAT, and coordinated by IMDEA Energía Energy, in Madrid. 

During the meeting, each Doctoral Candidate presented the main achievements and activities developed within their Individual Research Projects since the last meeting, showcasing the excellent progress being made across the programme. These sessions provided valuable discussions, feedback, and new perspectives, reinforcing the collaborative spirit of the project.  

Biorefinery for Biofuels & Chemicals Training 

The training was held in Turku, Finland. The three-day training provided an in-depth overview of modern biorefinery concepts and sustainable biomass valorization, covering topics such as lignocellulosic biomass processing, thermochemical conversion technologies, algae-based biorefineries, bioactive compounds, and industrial case studies from pilot-scale biorefineries.  

The workshop fostered interdisciplinary learning and collaboration while strengthening expertise in circular bioeconomy and sustainable production of biofuels and biochemicals.

 

 

 

 

 

 

 

 

EventNetworking
Machine Learning for Biosciences

PhD student Abdullah Nasir from the BioEng Lab research group participated in the 9th BioSpec Interdisciplinary Summer School in Machine Learning for Biosciences, organised by the Norwegian University of Life Sciences (NMBU). 

The aim of the summer school was to introduce the participants to the analysis of biological data using infrared spectroscopy and machine learning. Through lectures and a hands-on interdisciplinary project, it provided practical skills in FTIR data processing, spectral pre-treatment, multivariate analysis and machine-learning methods, while strengthening the ability to tackle complex bioscience problems collaboratively.  

These skills and insights are directly relevant to research involving biological samples and spectroscopic data. 

Defence
Oksana Tingajeva defended her MSc thesis

Congratulations!
Oksana Tingajeva, an MSc student in the Applied Chemistry and Biotechnology curriculum, has successfully defended her thesis “Rhodotorula toruloides bioprocess analysis for biopolymer production”.

Supervisor: Rahul Kumar, Senior Researcher – Department of Chemistry and Biotechnology
Co – supervisor: Henrique Sepulveda Del Rio Hamacek ,PhD student & Early Stage Researcher – Division of Food and biotechnology: Department of Chemistry and Biotechnology
Reviewer: Kaarel Adamberg, Senior Researcher – Division of Food and biotechnology: Department of Chemistry and Biotechnology

(Summary of the thesis)
Although Rhodotorula toruloides is widely studied for lipid production, its potential for exopolysaccharide (EPS) synthesis in bioreactor conditions remains underexplored. This study investigated how cultivation parameters—such as pH control, nutrient composition, and osmotic stress—affect biomass formation, EPS production, and cell morphology.

Bioreactor cultivations showed that buffered, pH-controlled, and urea-supplemented conditions significantly increased biomass (≈14–20 g L⁻¹), while control and high-salt conditions resulted in lower biomass (≈6–7 g L⁻¹). EPS production was highest under control and buffered conditions (≈3–4 g L⁻¹), with minimal production under other conditions. Protein content and morphology varied, with filamentous and aggregated structures observed under certain conditions, highlighting the influence of pH and nutrient balance on cellular adaptation.

Overall, the results demonstrate that cultivation conditions strongly impact biomass composition and EPS synthesis in R. toruloides, supporting its potential as a versatile platform for biopolymer production. Further research should focus on process optimization and molecular-level analyses to better understand EPS biosynthesis and carbon allocation.

This work provides a strong foundation for a planned scientific publication. 📄
We look forward to seeing where your passion for science will take you next! 🔬

GeneralProjects
1st place – Nucleate Baltics Genesis Demo Day 2026 at Deep Tech Atelier 2026

A special congratulations to our PhD student Subhasis Behera´s team BeeYOND for achieving 1st place in the competition – Nucleate Baltics Genesis Demo Day 2026 at Deep Tech Atelier 2026! 

Over the past months, talented and passionate innovators from across Latvia, Estonia, and Lithuania came together to transform scientific ideas into impactful biotech and deep tech solutions.  

BeeYOND idea was to create honey without bees—while preserving the same nutritional and functional benefits. Using locally sourced ingredients and precision fermentation, the team aims to produce a bee-free honey rich in enzymes and antioxidants.  

Wild honeybees are increasingly at risk of extinction across the EU, raising concerns about the long-term sustainability of traditional honey production. At the same time, the European honey market is projected to grow by 4.8% by 2030, driven by rising awareness of honey’s health benefits, including immune system support. Consumers are also shifting toward natural sweeteners over synthetic alternatives. 

Currently, local honey production meets only about 63% of demand, while up to 46% of imported honey is suspected to be adulterated. BeeYOND addresses both sustainability and quality challenges by offering a reliable and innovative alternative to conventional honey.  

“We need a sustainable source of honey without risking the honey-bee popluation.” 

 

Looking forward to tasting “Bee-Free-Honey” in the future! 

Defence
Andrei Jepifanov defended his MSc thesis

Congratulations! 
Andrei Jepifanov, an MSc student in the Applied Chemistry and Biotechnology curriculum, has successfully defended his thesis 
“Metabolic engineering strategies to address limiting xylose uptake in Rhodotorula toruloides“. 
 
SupervisorJuliano Sabedotti De Biaggi, Institute of Chemistry and Biotechnology, Researcher 
Reviewer: Evely Ojangu, Institute of Chemistry and Biotechnology, Engineer 
 
(Summary of the thesis) 
The non-conventional yeast Rhodotorula toruloides is a promising microbial cell factory due to its tolerance to harsh conditions and ability to utilize xylose—a key sugar in wood residues. Improving xylose metabolism could support more sustainable bioprocessing, although its efficiency still lags behind glucose. 
 
This study aimed to enhance growth on xylose by introducing heterologous pathway genes from Candida intermedia, Scheffersomyces stipitis, and Escherichia coli. Transformants were generated using the Lithium Acetate method and screened for growth performance, with gene insertion confirmed by PCR. 
 
While gene integration was successful, no significant improvement in xylose-based growth was observed. Variability among strains was likely due to random genomic integration via non-homologous end joining (NHEJ), as confirmed by PCR. 
 
Further research is needed to evaluate gene expression, analyze byproducts, and explore additional or combined pathway genes to improve xylose utilization and cell growth. 
 
We wish you exciting discoveries and continued success in your future projects!

Projects
YAF workshop on energy systems analysis

Our doctoral students, Subhasis Behera and Abdullah Nasir, participated in the two-day intensive YAF workshop dedicated to Energy Systems Analysis in Madrid, Spain, hosted by IMDEA Energy. The workshop introduced environmental life cycle assessment of energy systems with hands-on case studies.

During the two-day workshop, the curriculum covered:

  • Energy systems and process modelling
  • Environmental Life Cycle Assessment (E-LCA)
  • Life Cycle Costing (LCC)
  • Social Life Cycle Assessment (S-LCA)
  • Life Cycle Sustainability Assessment (LCSA)

On top of all, the host paid students a guided visit to IMDEA Energy’s laboratories and pilot plants, offering them a unique opportunity to explore cutting-edge research facilities and gain first-hand insight into ongoing innovations in renewable energy and sustainable technologies.

Defence
Alīna Reķēna defended her doctoral thesis

Alīna Reķēna successfully defended her doctoral thesis on the topic “Computational Design of Yeast-Based Cell Factories”.

The doctoral thesis supervisor was Associate Professor Petri-Jaan Lahtvee.

The thesis opponents were Professor Marija Cvijovic (Chalmers University of Technology) and Professor Emeritus Merja Penttilä (VTT Technical Research Centre of Finland).

Congratulations, Dr. Alīna Reķēna! We wish you exciting discoveries in your future projects! 🎉

Defence
Lev Kolesnikov defended his MSc thesis on simulated microgravity effect on yeast

Lev Aleksandr Kolesnikov, MSc student in Food Technology and Development, defended his thesis “Effect of simulated microgravity on yeast growth”. In his thesis, Lev investigated, in a three-dimensional clinostat, how simulated microgravity affects microorganisms, especially their phenotype, morphology, transcriptomics and gene regulation. Simulated microgravity was originally developed to replicate space-like conditions, although it cannot completely mimic space-like conditions, as extraterrestrial conditions also involve other contributing factors, such as radiation. It is, nevertheless, a good alternative for investigating space-like conditions in situations where true space experiments are not possible, and the technology is now evolving even beyond as a new method to alter physiological function in a non-invasive way to alter pathways relevant to health and industry.

The topic is of interest because it is known that the virulence of some microorganisms and the fermentation speed increase in microgravity. As microorganisms are an essential part of the human microbiome, understanding how they react, for example, during long space travels, provides valuable information for human health. The work was conducted in collaboration with Litegrav OÜ and supervised by Prof. Petri-Jaan Lahtvee and Srdjan Gavrilovic.

 

 

General
2nd-3rd price in safety challenge

In research, curiosity drives us forward — but safety keeps us grounded. Our laboratory considers safety utmost important.

We participated in a safety challenge organised by the TalTech Department of Chemistry and Biotechnology, where we won 2nd-3rd prize!

What was improved:
✅ Training video introducing the main safety principles in a bioengineering laboratory
✅ All safety guidelines were organised and made accessible via QR codes that are hung in the laboratory space
✅ Safety reporting form was implemented for easy access for reporting incidents, near misses and bad conduct

Event
2nd YAF Annual Meeting

Juliano Sabedotti de Biaggi, Abdullah Nasir and Subhasis Behera participated in the 2nd YAF Annual Meeting from 3rd to 7th November. The meeting and Professional Development Workshop were organised by Åbo Akademi University in Turku, Finland.

The participants continued their training provided by hfp Consulting, where they learned about emotional intelligence, active listening, leadership, conflict management and the importance of starting with “why” when explaining their research. On the second day, they received updates from each research project, allowing them to clearly see the progress each doctoral student is making. As always, it was great to meet the whole consortium to get a bigger picture of the project, not to mention how energising it is to engage with such a motivated and united group of students. We are grateful to hfp consulting for the insightful training and to Åbo Akademi University for the warm hospitality. It was an enriching experience, and we can not wait for the next one.

The project Yeast-Based solutions for Sustainable Aviation Fuels is funded by the European Union’s Framework Programme for Research and Innovation Horizon Europe (HORIZON) Marie Skłodowska-Curie Actions Doctoral Networks (MSCA-DN) under the Grant Agreement 101120389.

 

 

EventNetworking
6th Congress of Baltic Microbiologists

Juliano S. D. Biaggi and Alīna Reķēna attended the 6th Congress of Baltic Microbiologists in Riga, Latvia, from October 1st to 3rd.

Alīna made an oral presentation on the topic of Chemostats and Omics: Tools to Improve Lipid-producing Yeasts.

Juliano presented a poster and had a flash talk on the topic of Digitalisation of biology: the dawning of the Taltech Biofoundry.

The conference covered the great scope of microbiology research in the Baltics, from virology to biotechnology. The program was involving and allowed everyone to speak at the main stage. Even though it was centered in the Baltics, the conference also had attendees from Germany, Italy and the USA.

Juliano noted that the 6th CBM was a great opportunity to present the first steps of the Estonian Biofoundry in Taltech, as one of this project’s goals is to enhance regional development by extending the biosustainable research and industrial practices in the Baltic region. At the same time, it is always good to catch up on what our peers are working on, and to get out of the Biotech bubble to see that we a just part of a bigger research effort to make our world a better place in the long term.

Alīna noted that the Selection of talks highlighted the interdisciplinarity of microbiology research in the Baltic countries. Closer to our expertise, the sessions on microbial diversity and waste valorisation allowed us to learn more about microbes, their origin, and biotechnological applicability. She presented our work at the Metabolic Engineering and Systems Biology session on exploring metabolic mechanisms of lipid-producing yeast Rhodotorula toruloides for industrial applications.

The conference visit was funded from Grant Agreement No. 101060066, ‘Centre for Digitalisation of Biology Towards the Next-Generation of Biosustainable Products (DIGIBIO)’.
Photo credit: Kristaps Neiberts
 
Event
Scientist Night brought together children interested in science 👩‍🔬

The bioengineering team held two workshops on enzymes 🧪 Children and their parents had an opportunity to learn about enzymes and carry out three hands-on experiments to see how enzymes facilitate chemical reactions in real life.
*How pineapple juice coagulates milk proteins thanks to the enzyme bromelain 🍍
*How lactase tablets help in digesting lactose for those who are lactose intolerant 🥛
*How starch is digested in the mouth by the enzyme amylase found in saliva 👅

Among other things, the participants learned the basics of food analytics and measured pH and glucose content in milk.

The bioengineering team is always happy to inspire the next generation of future scientists!

Projects
President Alar Karis visits Bioengineering laboratory

Bioengineering laboratory had the honour of welcoming the president of the Republic of Estonia, Mr. Alar Karis, and his delegation to its premises.

According to Petri-Jaan Lahtvee, the laboratory’s associate professor, this visit allowed us to present the biotechnology advancements and innovations that take place in the laboratory. Furthermore, it was possible to present how automation is being implemented through projects.

This visit marks an endorsement of Estonian science and biotechnology. We are delighted to see that biotechnology is valued on the national level.

Photo by Enriko Pedaksalu.

Projects
Yeast Genetics and Genomics course at Cold Spring Harbor, New York

Alīna Reķēna took part in Yeast Genetics and Genomics course, from July 22 to August 12 at Cold Spring Harbor, New York, USA

The legendary yeast course at CSHL, with more than 50 years of history, offered lectures on the fundamentals of yeast genetics, daily seminars from leaders in the yeast community, and 10 laboratory experiments that showcase the methods needed in a modern-day yeast lab.

Lecture topics included yeast cell cycle, tetrad analysis, genetic interactions, genome sequencing, imaging and functional genomics.

The yeast community has pioneered many of molecular and genetic techniques we rely on today. The goal of experimental section was to provide with sufficient hands-on experience apply these techniques in our own laboratories – from classical and modern genetic approaches (mutant isolation and characterisation, tetrad analysis, complementation), to molecular genetics (yeast transformation, gene replacement, gene fusion and mutation), as well as use of the yeast deletion set, multiplex deep sequencing, cytological approaches (epitope tagging), and yeast cell imaging.

Many thanks to fellow course participants for exciting discussions and fun learning, to the seminar speakers for their insights and inspiration, and to the course instructors, teaching assistants and coordinators for their dedication and wisdom.

Photo credits: Constance Brukin

Event
YAF summer school brought together a diverse range of students working on sustainable aviation fuels

12 doctoral students who are part of YAF project gathered in Tallinn University of Technology for three days to learn about metabolic engineering. YAF project, funded by the European Union, aims to produce new generation of yeast-based sustainable aviation fuels via microbial means.

Over the course of three days the participants gained insight in molecular and synthetic biology, genotyping, phenotype screening, characterization and genome-scale modeling; and obtained hands-on experience in plasmid preparation and transformation.

After daily lectures there was time to share scientific gains and pains in an informal environment. The participants also had a chance to learn about the History of Tallinn and experience traditional Estonian socializing activities such as sauna.

It was a diverse scientific and cultural experience, which gathered students from seven partner organizations: Institute Imdea Energy (IME), Tallinn University of Technology (TUT), Technical University of Denmark (DTU),  Åbo Academy University (ABO), Centro de Investigaciones Energeticas Medioambientales y Tecnologicas (CIEMAT), Bio Base Europe Pilot Plant (BBEPP) and Imperial College London (ICL)

We are very happy to have welcomed such a great team of young scientists and thank Juliano Sabedotti de Biaggi, Srdjan Gavrilovic and Kaisa Orgusaar for organizing the summer school.

Projects
New Generation Aviation Fuels

Have a look at how the aviation fuel industry is being transformed in the Bioengineering laboratory in this newly published video!

Our doctoral researchers Abdullah Nasir and Subhasis Behera are working committedly to make the aviation fuels more sustainable. They are engineering metabolic steps for the biosynthesis of energy-rich monoterpene intermediates from biowaste that are fit to be used as raw material in aviation fuel production.

Open positions
New PhD postion is opened in collaboration with TFTAK!
Open PhD Position in Enzyme Engineering 🔬
📍 TalTech Bioengineering Lab x TFTAK | Tallinn, Estonia
We’re excited to announce a PhD position in Enzyme Engineering focused on a systematic approach toward high-level protein production in yeast.
This is a collaborative project between the Bioengineering Lab at TalTech and TFTAK, combining cutting-edge research in strain engineering and enzyme design.
What we’re looking for:
If you’re interested in:
✅ High-throughput strain engineering
✅ Synthetic biology & enzyme design
✅ Scalable protein production in yeast
…then this could be the opportunity for you!
📅 Starting date: September, 2025
application deadline: June 30th 2025 23:59 EET

The Food Tech and Bioengineering laboratory at Tallinn University of Technology (TalTech) is focused on developing sustainable solutions in the bioeconomy sector. Led by Professor Petri-Jaan Lahtvee, the lab specializes in bioinformatics, metabolic engineering, and bioprocess optimization. Research efforts are directed towards creating microbial cell factories to convert waste materials into valuable products, with a focus on biosustainability and the sustainable production of food, feed, bio-chemicals, and materials.

TFTAK (Center of Food and Fermentation Technologies) is a leading Estonian R&D center specializing in innovative solutions for the food, biotech, and fermentation industries. Its fermentation competencies cover from strain development and metabolic engineering to precision fermentation and process scale-up. Dr. Steven van der Hoek’s group develops synthetic biology tools and strain engineering capabilities, focusing on precision fermentation for alternative protein production, combining systems biology, bioprocess engineering, and high-throughput screening.

Role Description

This is a full-time on-site Doctoral Researcher role shared between Bioengineering and Food laboratory in Tallinn University of Technology and TFTAK. The doctoral researcher will be involved in tool development for reliable protein production pipeline from concept to gram scale. Duties will include participating in the Design-Build-Test-Learn cycle of cell factory design and process development, as well as collaborating on projects for creating microbial cell factories.

Qualifications

  • Research experience in bioinformatics, metabolic engineering, or bioprocess optimization
  • Strong analytical and problem-solving skills
  • English at least B2 level
  • Ability to work in a collaborative multicultural research environment
  • Excellent communication and presentation skills
  • Master’s degree in life sciences
  • Master´s degree in bioengineering, bioinformatics, or related field is a plus
  • Experience in programming in Phyton and omics data analysis is a plus
  • Experience with cell factory design and optimization is a plus
  • Estonian language is a plus
  • Foreign applicants must have a valid Estonian residence permit or right of residence and a permanent legal income in accordance with the provisions of the Aliens Act.

What we offer

  • A fully funded 4-year PhD position starting in September 2025
  • Gross monthly salary starting from 2300 €
  • 35 calendar days of paid vacation yearly
  • Additional benefits including paid sick leave and health insurance
  • Flexible working hours and supportive supervision
  • Access to state-of-the-art laboratory facilities and high-throughput platforms
  • Opportunity to work in a dynamic, interdisciplinary environment bridging academia and industry
  • International research collaboration and opportunities for mobility
  • Personal and professional development through conferences, courses, and workshops
  • The chance to contribute to meaningful innovation in sustainability and synthetic biology

Applying

For more info and applying please submit your CV and documents via: https://taltech.glowbase.com/positions/977

More info about applying for a PhD position in Tallinn University of Technology can be found at https://taltech.ee/en/phd-admission