Available research topics:
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The influence of ecological factors on the quiescent state of the yeast S. cerevisiae: from individual cell characteristics to population dynamics
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.
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PhD Programme in Biology
Admission to the PhD Programme in Biology
in the Doctoral School of Exact and Natural Sciences
language of education: English
The PhD Programme in Biology is carried out in English, in a full-time, eight-semester system.
This PhD programme covers courses representing various areas of biological sciences, including training in modern methodology and mastering skills useful in professional academic and non-academic careers. Choice of facultative classes and the possibility of gaining credits for courses offered outside of the University ensures flexibility and helps to adjust participation in courses to the individual research plan of the student.
For everyone who will be accepted for the PhD programme in Biology, a scholarship is guaranteed.
PhD students are recruited for the specific research topics offered by the faculty members. We kindly ask you to follow the recruitment rules described in each competition.
Each year, PhD students and their advisors/promotors write an individual research plan for a given year. Until the end of four semesters, students’ achievements are evaluated (mid-term evaluation) by the committee.
Doctoral dissertations are prepared under the supervision of a scientific staff of the Faculty of Biology (members of the Institute of Botany, Institute of Environmental Sciences or Institute of Zoology and Biomedical Research). PhD programme in Biology leads to the scientific Doctoral title in the discipline of biology. More information about the programme can be found here.
See also:
Faculty of Biology website.
A subpage dedicated to this education programme.
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Nested Portlets
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How to apply?
- Check the admissions schedule.
- Read the rules and detailed conditions of admission.
- Collect the required documents.
- Apply in the Online Application System (IRK).
- see instructions on how to apply in IRK,
- please note: registration will start on 21st May, before this date no enrolments for our School are displayed in the IRK system.
- Take the exam.
- Make an enrolment in the Doctoral School.
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Admission schedule
for PhD Programme in Biology education programme
1st round
- 21. May 2024 – Opening of registration in IRK System
- 23. June 2024 – Closing of registration in IRK System
- 28. June- 4 lipca 2024 – Entrance exams
- 4. July 2024 – Committee meeting
- 8. July 2024 – Announcement of results
- 9-30. July 2024 – Enrollment to the Doctoral School*
- 31. July 2024 – Enrolment in the Doctoral School from the reserve list*
*enrollment possible during working hours of Secretariats of the Education Programmes
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Admission limits
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1st round – 10 doctoral students
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Contact
Secretariat of the Education Programme
mgr inż. Anna Stec
tel.: (0048) 12 664 6752
e-mail: wb.doktoranci@uj.edu.pl
Head of the Education Programme
dr hab. Joanna Kapusta, prof. UJ
tel.: (0048) 12 664 5206
e-mail: joanna.kapusta@uj.edu.pl
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The information presented on this subpage applies to admission for the academic year 2024/25. Documents such as admission rules, list of required documents, education programme and others may change in the next admission. Most documents differ for each education programme. Always check the documents on the sub-page of the programme to which you are applying.