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>> Program kształcenia - PhD Programme in Biology <<

>> Program kształcenia - PhD Programme in Biology [rok akademicki 2023/2024] <<

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. Some of the competitions listed below are held outside the OAS system (Online Application System). 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.

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Evolution of the optimal level of gene expression. (Institute of Environmental Sciences)

Institute: Institute of Environmental Sciences

Topic: Evolution of the optimal level of gene expression

Name of supervisor:

Katarzyna Tomala

Background information:

The project tests assumptions of two related hypotheses regarding the evolution of dominance: safety margin and optimal expression. The increased safety margin hypothesis proposes that the expression level of enzymes in the standard conditions is too-high to ensure proper organism function in a harsh or frequently changing environment. The optimal expression model proposes that the wild-type protein doses are optimal, but the fitness decreases very slowly for the vast range of protein doses, including the halved one.
The essential assumption of these hypotheses of dominance is that natural selection efficiently shapes the expression of individual genes. The expression pattern observed in a frequently encountered environment should be a well-adapted organism’s characteristic. Furthermore, the longstanding selection for the new environment should lead to expression adjustments. Indeed, laboratory evolution experiments with bacteria have shown that expression of the LacZ gene approached its predicted optimal value (different for different lactose concentrations). However, other studies have found that the selection coefficients of mutations changing expression are extremely small or even suggest that divergence in expression patterns observed between closely related species can be effectively neutral – gene expression follows phylogeny and not the environments.

The main question to be addressed in the project:

How likely selection is to fine-tune the expression level to the optimal value and whether the expression safety margin will emerge in the changing environment?

Information on the methods/description of work:

Laboratory evolution of the yeast strains with an engineered suboptimal (too-low or too-high) and native (control) expression level of the TDH3 gene. Two growth regimes will be applied: with constant and changing glucose concentrations. Investigation of the evolved lines and evaluation:
  • how often TDH3 expression changes (increase in case of too-low and decrease for too-high expression strains) explains the increase in strains' growth rate;
  • whether evolved TDH3 expression is, on average, higher for strains evolved in the variable glucose regime (test of the safety-margin hypothesis).

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

  • MSc in biology or related fields
  • ability to work with microorganisms
  • experience with flow cytometry would be advantageous.
Place/name of potential foreign collaborator: -

References (max.3):

  1. D. Bourguet, “The evolution of dominance,” Heredity, vol. 83, no. 1, Art. no. 1, Jul. 1999, doi: 10.1038/sj.hdy.6885600.
  2. L. D. Hurst and J. P. Randerson, “Dosage, Deletions and Dominance: Simple Models of the Evolution of Gene Expression,” J. Theor. Biol., vol. 205, no. 4, pp. 641–647, Aug. 2000, doi: 10.1006/jtbi.2000.2095.
  3. F. Duveau et al., “Fitness effects of altering gene expression noise in Saccharomyces cerevisiae,” eLife, vol. 7, p. e37272, Aug. 2018, doi: 10.7554/eLife.37272.
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