Adaptive Immunity

Project Description:

The group of Adaptive Immunity has a strong publication record in the field of T-cell biology. Recently, we have introduced single cell RNA transcriptomics and analysis of antigenic receptors to uncover and characterize novel T-cell subsets, including their antigenic specificity. Within the project, the student will analyze unique single T-cell data (transcriptomics, ATACseq, repertoire) from animal models of immunological diseases (infection, cancer, autoimmunity) and/or human patients. Moreover, the student will develop novel tools for these analyses. The inclusion of experimental wet work in this project is optional, depending on the preferences and background of the selected candidate.

We offer high scientific standards in the amazing field of T-cell-mediated immunity and the environment of a young, but experienced, lab. The student with receive full time salary according to IMG standards and the stipend from the affiliated university.

Candidate Profile:

We are looking for an enthusiastic early career scientist who wants to use their programming skills to tackle biological problems in our multidisciplinary team. The candidate should show high level of independence and problem solving skills in programming/bioinformatics. However, they should be able to collaborate with experimental scientists within our interdisciplinary team as well.

The successful candidate has a master’s degree (or is close to its completion) in bioinformatics, computational science, biological, or chemical sciences. The candidate should have the prior experience with the analysis of large biological data and/or computational modeling of biological processes.

Only candidates, who directly contact the PI (ondrej.stepanek@img.cas.cz) before 28.2.2022 will be considered for the interviews.

Suggested reading:

• https://www.biorxiv.org/content/10.1101/2021.11.10.467495v2
• https://www.embopress.org/doi/full/10.15252/embj.201798518
• https://adaptiveimmunity.img.cas.cz/publications/

Project Description:

The group of Adaptive Immunity has a strong publication record in the field of T-cell biology. One of our long-term interests is uncovering the diversity of T-cell subsets with unique functions. This PhD project in experimental immunology focuses on the tissue infiltrating protective T cells (e.g., tissue resident memory T cells) and pathogenic T cells inducing damage to host tissues, which arise during bacterial and viral infections. The student will use the state-of-the-art methods (scRNAseq, mouse models of infection, flow cytometry) to characterize T-cells in tissues. In the next step, they will analyze the biological role of these subsets using our model systems for generating monoclonal T-cells.

We offer high scientific standards in the amazing field of T-cell-mediated immunity and the environment of a young, but experienced, lab. The student with receive full time salary according to IMG standards and the stipend from the affiliated university.

Candidate Profile:

We are looking for an enthusiastic early career scientist who wants to tackle the fundamental roles of T cells in infections. The candidate should show high level of problem solving skills and the ability to collaborate within our interdisciplinary team.

The successful candidate has a master’s degree (or is close to its completion) in life-sciences. Prior experience with experimental lab work is required (e.g., within a master’s diploma research project).

Only candidates, who contact the PI (ondrej.stepanek@img.cas.cz) directly before 28.2.2022 will be considered for the interviews.

Suggested reading:

• https://www.biorxiv.org/content/10.1101/2021.11.10.467495v2
• https://www.embopress.org/doi/full/10.15252/embj.201798518
• https://adaptiveimmunity.img.cas.cz/publications/

Location
Prague, Czech Republic, Central Europe
The Lab of Adaptive Immunity at the Institute of Molecular Genetics of the Czech Academy of Sciences headed by Ondrej Stepanek focuses on the T-cell signaling, T-cell diversity, and T-cell fate decisions.

Molecular mechanisms of Bardet-Biedl Syndrome
Bardet-Biedl syndrome (BBS) is a rare hereditary disease belonging to a group of ciliopathies, i.e., syndromes caused by a dysfunction of primary cilia. Primary cilia are specialized cellular organelles that function as cellular antennae by perceiving extracellular stimuli and transducing them through a multitude of signalling cascades. In our laboratory, we study the primary cilia and the BBSome complex, which facilitates transport of various signaling receptors into and out of the cilium. The BBS1 subunit is mutated most frequently and currently 24 BBS-causative mutations in BBS1 were identified in human patients.
The aim of this project is the identification of the pathology of the individual human mutations on the molecular and cellular level. The student will characterize the pathogenic BBS1 variants in our established cell line models. The analysis will include fluorescence microscopy techniques and methods of molecular biology.

We are looking for an ethusiastic student of cell biology, molecular biology, biochemistry or a related field who is motivated to work on a project with biological and medicinal relevance. Bachelor students are also very welcome.

We offer

• The project is tailored for MSc. student with a high chance of a publication in an international journal.
• The student will master multiple modern techniques of cell biology, molecular biology and microscopy.
• We are a young research group with a strong publication record.
• Excellent infrastructures of the Institute of Molecular Genetics.
• Overall, this position is a perfect step towards your career in life-science.

How to proceed
If interested, please, contact the supervisor Dr. Martina Huranová (martina.huranova@img.cas.cz).

Further reading

1. Niederlova V, Modrak M, Tsyklauri O, Huranova M*, Stepanek O*: Meta-analysis of genotype-phenotype associations in Bardet-Biedl Syndrome uncovers differences among causative genes. Hum Mutat. 2019 Nov;40(11):2068-2087. 
2. Prasai A, Schmidt Cernohorska M, Ruppova K, Niederlova V, Andelova M, Draber P, Stepanek O*, Huranova M*:The BBSome assembly is spatially controlled by BBS1 and BBS4 in human cells. J Biol Chem. In press. 
3. Tsyklauri O, Niederlova V, Forsythe E, Drobek A, Prasai A, Sparks K, Trachtulec Z, Beales PL, Huranova M*, Stepanek O*: Altered hematopoietic system and self-tolerance in Bardet-Biedl Syndrome. BioRxiv, doi: 2020.02.24.962886