Category: Defence

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! 🔬

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“. 
 
Supervisor: Juliano 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!

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! 🎉

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.

Three undergraduate students successfully defended their theses that were conducted under the bioengineering laboratory.

• Kristjan Pals, BSc in gene technology 2024 “Phosphoketolase gene knockout by CRISPR/Cas9 in nonconventional yeast Rhodotorula toruloides” supervised by Alīna Reķēna
• Maive Hanni, BSc in gene technology 2024 “Comparison of genome-scale metabolic models for investigating lipogenesis metabolism in Rhodotorula toruloides” supervised by Alīna Reķēna
• Oksana Tingajeva, BSc in gene technology 2024 “Rhodotorula toruloides’ exopolysaccharides: production, optimization and characterization” supervised by Rahul Kumar and Henrique Sepulveda del Rio Hamacek.

The students noted that conducting theses in the bioengineering laboratory gave them valuable experience on how laboratory work is conducted and good time management skills. They learned how to investigate metabolism in silico, improving their programming skills in Python. R. toruloides is a notable lipid producer and knowing the more specific metabolic pathways allows creation of more efficient microbial cell factories. The theses are part of a wider picture which aims producing oils such as palm oil and biodiesel in a more sustainable way.

Read the full theses in TalTech digital library:

1. Fosfoketolaasi geeni väljalülitamine CRISPR/Cas9 meetodil mittekonventsionaalses pärmis Rhodotorula toruloides – TalTech raamatukogu digikogu

2. Ülegenoomsete metaboolsete mudelite võrdlus Rhodotorula toruloides lipogeneesi uurimiseks – TalTech raamatukogu digikogu

3. Rhodotorula toruloides’i Eksopolüsahhariidid: tootmine, optimeerimine ja iseloomustus – TalTech raamatukogu digikogu