Supervisor: dr hab. Dominika Włoch-Salamon (dominika.wloch-salamon@uj.edu.pl)

Institute of Environmental Sciences

Background information:

What do cells do when they don't divide? Well, most living cells on Earth spend their lives in a state of quiescence. Quiescence is a reversible, deliberate pause in cell divisions that cells can return from. Therefore, despite its ubiquity, quiescence is much less studied than cell growth and divisions. Recent research shows that, unlike the traditional view, quiescent cells are not like a frozen 'Sleeping Beauty' but rather like 'Little Red Riding Hood,' energy demanding living systems that interact, communicate, and respond to both biotic and abiotic factors. Ecological factors such as temperature changes, nutrient availability, toxin presence, and social interactions contribute to cell diversity in the quiescent state in populations. As time spent in quiescence passes, quiescent cell characteristics change, eventually leading to the inability to return to divisions, culminating in cell death. To fully understand the dynamics of quiescence and its adaptability, we aim to conduct research at both the single-cell and population levels. We use Saccharomyces cerevisiae as a model organism. It's the only verified eukaryotic organism from which we can relatively easily obtain individual quiescent cells and their entire multimillion population, making yeast an ideal organism for studying quiescence at both the cellular and population levels.

The main question to be addressed in the project:

We aim to answer research questions such as:

How does the aging process occur for single cells and populations remaining in quiescence for different durations?

How do cell interactions and nutrient recovery from the environment influence population diversity during quiescence and aging at both the single-cell and population levels?

What are the genetic bases of adaptation to long and short periods of dormancy, including genes with unknown functions?

What are the evolutionary trade-offs associated with population heterogeneity in the context of long and short quiescence?

How do these processes depend on population density?

What ecological conditions lead to increased phenotypic diversity evolution?

Information on the methods/description of work:

The motivation behind this project is the gap in the current understanding of cellular quiescence and its interaction with the social and abiotic environment. To address these, our team will employ a combination of cellular (microscopy, cytometry, with hope for microfluidics), population (spectroscopy, experimental evolution), genetic (genetically modified microorganisms), and genomic (next-generation sequencing) techniques.

Additional information (e.g Special requirements from the student):

PhD degree in biology, biotechnology, bioinformatics or similar studies - knowledge or interest of the R or python programming language (at least at the basic level) - basic knowledge of next generation sequencing (NGS) data analysis; - knowledge of the basic principles of work in a microbiology laboratory - knowledge of basic techniques of molecular biology, microscopy; - interest in fluorescence microscopy and microfluidics; - passion for science, experiments and data. - willing to spend some time abroad (collaboration with CNRS France) - good communication skills.

Place/name of potential foreign collaborator:

IBGC, CNRS Bordeaux, France/ Isabelle Sagot and Damien Laporte

References:

[1] M Opalek, B Smug, M Doebeli, D Wloch-Salamon. (2022). On the ecological significance of phenotypic heterogeneity in microbial populations undergoing starvation. Microbiology Spectrum 10 (1), e00450-21

[2] Breeden, L. L., & Tsukiyama, T. (2022). Quiescence in Saccharomyces cerevisiae. Annual Review of Genetics, 56, 253-278.

[3] Sagot, I., Laporte, D. (2019). The cell biology of quiescent yeast–a diversity of individual scenarios. Journal of Cell Science, 132(1), jcs213025.