Topics Life Sciences

Life Sciences

1. Characterization of cyclin-dependent kinase 12 (CDK12) substrates and their roles in regulation of transcription and tumorigenesis

Supervisor: Mgr. Dalibor Blažek, Ph.D.

RG: Dalibor Blažek Research Group

Keywords: CDK12, transcription, mRNA processing, RNA polymerase II, cancer, genomics, proteomics, kinase inhibitors

2. Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression and tumorigenesis

Supervisor: Mgr. Dalibor Blažek, Ph.D.

RG: Dalibor Blažek Research Group

Keywords: CDK11, transcription, mRNA processing, RNA polymerase II, cancer, genomics, proteomics, kinase inhibitors

3.  Computational simulations of the conformational changes within Tau protein and its fibrilization

Supervisor:  doc. RNDr. Mgr. Jozef Hritz, Ph.D.

RG:  Protein Structure and Dynamics

Keywords:  computational simulations, molecular dynamics, coarse-grained simulations, Tau protein, neurodegenerative diseases

4.  Tau conformational changes induced by phosphorylation, truncation, and 14-3-3 proteins relevant in neurodegenerative diseases

Supervisor:  doc. RNDr. Mgr. Jozef Hritz, Ph.D.

RG:  Protein Structure and Dynamics

Keywords:  Tau protein, intrinsically disordered proteins, phosphorylation, 14-3-3 proteins, NMR spectroscopy, neurodegenerative diseases

5.  Development of bioinformatics methods for analyzing RNA modifications with long-read nanopore sequencing

Supervisor:  Mgr. Vojtěch Bystrý, Ph.D.

RG:  Bioinformatics Core Facility

Keywords:  Bioinformatics, long-read sequencing, nanopore, epitranscriptome, direct RNA sequencing.

6.  Designing modified DNA fragments

Supervisor:  prof. RNDr. Radek Marek, Ph.D.

RG: Radek Marek Research Group

Keywords:  DNA, base pairing, molecular modelling, quantum chemistry.

7.  Structure of parallel forms of nucleic acids: NMR spectroscopy and molecular modeling

Supervisor:  prof. RNDr. Radek Marek, Ph.D.

RG:  Radek Marek Research Group

Keywords:  NMR spectroscopy, DNA, base pairing, molecular modelling.

 8. Microenvironment models and their use to study agressivness and targeted therapy in B cell malignancies

​Supervisor:  doc. MUDr. Mgr. Marek Mráz, Ph.D.

RG:   Marek Mraz Research Group

Keywords:   lymphoma, microenvironment, models

9.   Long non-coding RNAs (lncRNAs) in the pathogenesis of mature B cell malignancies

​Supervisor:   doc. MUDr. Mgr. Marek Mráz, Ph.D.

RG:   Marek Mraz Research Group

Keywords:  Long non-coding RNA, lymphomas, DLBCL, miRNA

10.   Investigating pre-mRNA alternative splicing during the embryonic thermoresponse in Arabidopsis thaliana

​Supervisor:   Helene Robert Boisivon, Ph.D.

RG:    Helene Robert Boisivon Research Group

Keywords:  Arabidopsis thaliana, embryogenesis, high temperatures, alternative splicing

11. Dishevelled internal affairs in Wnt signalling

Supervisor: Konstantinos Tripsianes, Ph.D.

RG: Konstantinos Tripsianes Research Group

Keywords: Wnt signalling, Dishevelled, Casein kinase, interactions, conformations, phosphorylations, dynamics, allostery, NMR, X-ray crystallography, SAXS, FRET, cryo-EM, native MS, MS-HDX.

12. Phage infection of biofilm

Supervisor: doc. Mgr. Pavel Plevka, Ph.D.

RG: Pavel Plevka Research Group

Keywords: Virus, phage, structure, cryo-EM, cryo-ET, LSFM, light sheet fluorescence microscopy, biofilm, staphylococcus, phage therapy.

13. Structural study of enterovirus replication in situ

Supervisor: doc. Mgr. Pavel Plevka, Ph.D.

RG: Pavel Plevka Research Group

Keywords: Virus, structure, cryo-EM, cryo-ET, replication, assembly, capsid, replication factory, membrane, replicase.

14. Restoring antiviral properties of mammalian Dicer

Supervisor: prof. Mgr. Richard Štefl, Ph.D.

RG: Richard Štefl Research Group

Keywords: RNA biology, RNA viruses, structural biology, antiviral therapy.

15. Correlative light and electron microscopy of transcription condensates

Supervisor: prof. Mgr. Richard Štefl, Ph.D.

RG: Richard Štefl Research Group

Keywords: CLEM, cryo-EM, organization of transcription, phase separation.

16. Terminal RNA modifications in gene expression and viral infection

Supervisor: prof. Mgr. Štěpánka Vaňáčová, Ph.D.

RG: Štěpánka Vaňáčová Research Group

Keywords: RNA modifications, RNA processing, transcriptomics, proteomics, protein-RNA interactions.