We would like to congratulate the following PhD students who have defended their theses. Good luck in your future endeavors!

Kaspar Koolmeister

On 19 February 2026, Kaspar Koolmeister defended his PhD thesis, “Stomatal CO₂ Regulation Pathway and Its Application for Modulating Tomato Plants,” supervised by Professor Hannes Kollist and Associate Professor Hanna Hõrak from the University of Tartu. His opponent was Professor Matthew Gilliham from the University of Adelaide (Australia).

In his doctoral thesis, guard-cell CO₂ signalling and its function in Arabidopsis thaliana were studied across different CO₂ concentration ranges and under normal and low air humidity. A key role for the mitogen-activated protein kinases MPK12 and MPK4 in stomatal CO₂ regulation was identified. More info: https://dspace.ut.ee/items/13693e48-2889-491c-85d6-ec1ac8d5239e

Photo: Kaspar Koolmeister

Egon Meigas

On 25 August 2026, Egon Meigas defended his PhD thesis, “Evolution of Gas Exchange Traits and Their Application in Crop Breeding,” supervised by Associate Professor Ebe Merilo, Professor Hannes Kollist, and Associate Professor Dmitry Yarmolinsky from the University of Tartu. His opponent was Research Fellow Diego Márquez from the University of Birmingham (United Kingdom).

This doctoral research investigated how plants regulate water loss through stomata in response to drought, air humidity, and the hormone ABA. Studies in horsetails and barley revealed key evolutionary and molecular mechanisms of stomatal regulation, while research on spring wheat identified promising genotypes and developed a rapid field method for measuring gas exchange. These findings support the development of more drought-resilient and water-efficient crops. More info: https://dspace.ut.ee/items/44584995-bc86-4bca-b71d-87c1ad640d91

Kait Kaarel Puss

On 27 August 2026, Kait Kaarel Puss defended his PhD thesis, “Ultrasound Processing of Forest Biorefinery Lignin and Lignin-Cellulose Mixtures,” supervised by Associate Professor Ilona Faustova from the Institute of Bioengineering and Associate Professor Siim Salmar from the Institute of Chemistry, University of Tartu. His opponent was Professor Christos Argirusis from the Laboratory of Inorganic Materials Technology, School of Chemical Engineering, National Technical University of Athens (Greece).

This doctoral thesis investigated how power ultrasound can be used to process two materials produced in a wood biorefinery: lignin and a lignin-cellulose mixture. Ultrasound at 20 kHz creates rapidly forming and collapsing bubbles in liquids, producing strong local mechanical forces. The work examined whether these forces could improve lignin dissolution, modify lignin-cellulose mixtures, and reveal how lignin affects the response of cellulose to ultrasound. More info: https://dspace.ut.ee/items/8312dbbf-bca2-4063-aeca-1ce9f9c24527

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

On the 20^th February, 2026, 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, Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia. The thesis opponents were Professor Merja Penttilä, VTT Technical Research Centre of Finland, Espoo, Finland and Professor Marija Cvijovic, Department of Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden.

The development of sustainable biomanufacturing increasingly depends on the ability to design and optimize microbial cell factories using computational approaches. Yeasts are versatile eukaryotic hosts with robust growth, advanced genetic tools, and extensive industrial applications. Genome-scale metabolic models (GEMs) have become valuable tools for predicting cellular metabolism and guiding the production of fuels, organic acids, pharmaceuticals, flavours, fragrances, and other bioproducts. Since the first GEM of Saccharomyces cerevisiae was developed in 2003, such models have been continuously expanded and refined, including the community-curated Yeast9 model released in 2024.

Despite these advances, conventional GEMs have limited predictive power because they generally do not account for the finite capacity of the cellular proteome, enzyme kinetics, or regulatory mechanisms. These limitations are particularly important for nonconventional yeasts, such as the lipid-producing Rhodotorula toruloides, for which experimental data are relatively scarce, and assumptions based on S. cerevisiae may not be applicable.

In Alīna’s thesis, genetic, biochemical, and computational approaches were combined to develop and validate enzyme-constrained GEMs (ecGEMs) of S. cerevisiae and R. toruloides. Quantitative proteomics, physiological measurements from controlled growth experiments, and genetic perturbations were integrated to parameterize and evaluate the models. S. cerevisiae was used as a benchmark for testing model performance under different environmental conditions, while R. toruloides provided a case study for extending enzyme-constrained modeling to a nonconventional, lipid-accumulating yeast.

The results demonstrated that ecGEMs can capture proteome limitations and substrate-dependent metabolic allocation, while also revealing systematic deviations caused by current model assumptions. The work provided new insights into energy and redox balance in yeast, identifies key data requirements for modeling unconventional species, and demonstrates how integrating quantitative proteomics with genome-scale modeling can support more predictive and rational design of future microbial cell factories.

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

Read more here: https://bioeng.taltech.ee/5533-2/