Dissertation Topics

Topics for the call SPRING 2021

Bio-omics


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

Supervisor : Dalibor Blažek

RG : Dalibor Blažek Research Group

Keywords : transcription, DNA damage, cancer, genomics, proteomics


2. Functions of cyclin-dependent kinase 11 (CDK11) in regulationof gene expression

Supervisor : Dalibor Blažek

RG : Dalibor Blažek Research Group

Keywords : CDK11, histone genes, cancer, proteomics, genomics


3. Plant telomeres and telomerases

Supervisor : Jiří Fajkus

RG : Jiří Fajkus Research Group

Keywords : Telomeres, telomerase, RNA-protein interactions, bioinformatics, evolution


4. REGULATION OF BCR SIGNALLING BY DNA DAMAGE RESPONSE AND P53 PROTEIN

Supervisor : Marek Mráz

Co-supervisor : Miroslav Boudný

RG : Marek Mráz Research Group

Keywords : B-cell receptor signaling, BCR, leukemia, lymphoma, B cell malignancies,
miRNAs, p53, FOXP1, CD22 sh, CLL


5. LONG NON-CODING RNAs (lncRNAs) IN LEUKEMIAS

Supervisor: Marek Mráz

RG : Marek Mráz Research Group

Keywords : Follicular lymphoma, FL, non-Hodgkin lymphoma, B-cell lymphoma, NGS,
Illumina, genome editing, CRISPR, DLBCL, leukemia, CLL, FCR, BCR signaling
inhibitors


6. REGULATION OF CELL MIGRATION IN B CELL LEUKEMIAS ANDLYMPHOMAS

Supervisor : Marek Mráz

RG : Marek Mráz Research Group

Keywords: Follicular lymphoma, FL, non-Hodgkin lymphoma, B-cell lymphoma, NGS,
Illumina, genome editing, CRISPR, DLBCL, leukemia, CLL, FCR, BCR signaling
inhibitors


7. ROLE OF TRANSCRIPTION FACTORS IN ONSET AND PROGRESSIONOF B-CELL MALIGNANCIES

Supervisor : Marek Mráz

Co-supervisor : Josef Večeřa

RG : Marek Mráz Research Group

Keywords: leukemia, lymphoma, B cell malignancies, TFs, CLL3


8. Subcellular trafficking in plant survival

Supervisor : Tomasz Nodzynski

RG : Tomasz Nodzynski Research Group

Keywords: vesicular trafficking; intracellular localization; stress response; adaptation


9. Investigating the regulation of the RNA modifying enzyme ADAR1 and how it regulates other biological pathways and diseases

Supervisor : Mary O’Connell

RG : Mary O’Connell Research Group

Keywords: RNA modification, epitranscriptome, ADAR, innate immunity, cancer


10. Complexes Maintaining Chromatin Structure

Supervisor : Jan Paleček

RG : Jiří Fajkus Research Group

Keywords: Chromatin structure, genome stability, SMC complexes


11. Proteins involved in the regulation of telomeric repeats

Supervisor : Petra Prochazkova Schrumpfova

RG : Jiří Fajkus Research Group

Keywords: telomerase; telomeres; proteins; telo-box; regulatory elements; telomerase assembly; plant
development


12. The use of CRISPR/Cas9 technology to developinnovative strategies for cellular therapy ofhematological malignancies

Supervisor : Michal Šmída

RG : Michal Šmída Research Group

Keywords: CRISPR/Cas9, CAR-T cell, B-cell malignancy, genetic screening


13 . The role of protein-protein interactions in the dynamics of m6A RNA modification

Supervisor : Štěpánka Vaňáčová

RG : Štěpánka Vaňáčová Research Group

Keywords: mRNA, protein interactions, m6A RNA, m6Am, RNA modification



Structural Biology


1. Structal studies of various states of direct and bridged transcription-translation coupling in vitro and in vivo

Supervisor : Gabriel Demo

RG : Gabriel Demo Research Group

Keywords : RNA polymerase, ribosome, coupling, structure, cryo-EM, cryo-ET


2. Determination of structural mechanism of coupledviral transcription and host translation in virusinfected mammalian cells

Supervisor : Gabriel Demo

RG : Gabriel Demo Research Group

Keywords : Poxviruses, viral RNA polymerase, ribosome, coupling, cryo-ET


3. RNA as a drug target

Supervisor : Peter Lukavsky

RG : Peter Lukavsky Research Group

Keywords : mRNAs, 3’UTRs, non-coding mRNA


4. Designing modified DNA fragments

Supervisor : Radek Marek

RG : Radek Marek Research Group

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


5. Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling

Supervisor : Radek Marek

RG : Radek Marek Research Group

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


6. Structural and time-resolved studies of phage replication in bacterial biofilm

Supervisor : Pavel Plevka

RG : Pavel Plevka Research Group

Keywords : bacterial biofilm, phage therapy, ion beam milling, cryo-electron tomography, cryo-ET,
fluorescence microscopy, cryo-electron microscopy, virology, antibiotic-resistance


7. Structural study of enterovirus replication in vivo

Supervisor : Pavel Plevka

RG : Pavel Plevka Research Group

Keywords : enteroviruses, replication cycle, ion beam milling, cryo-electron tomography, cryo-ET, virology,
cryo-electron microscopy


8. Structural Biology of WNT Signalling

Supervisor : Konstantinos Tripsianes

RG : Konstantinos Tripsianes Research Group

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


9. Association of proteins in phospholipid membranes

Supervisor : Robert Vácha

RG : Robert Vácha Research Group


10. Selectivity of translocation across lipid membranes

Supervisor : Robert Vácha

RG : Robert Vácha Research Group


11. Structural characterization of hybrid proteinsinvolved in neurodegenerative diseases

Supervisor : Jozef Hritz

Consultant : Lukáš Žídek

RG : Lukáš Žídek Research Group

Keywords : hydrid proteins, disordered region, NMR spectroscopy, neurodegenerative diseases
phosphorylation, computational simulations


12. Structural properties of human carbonic anhydrase IX and design of its inhibitors

Supervisor : Jozef Hritz

RG : Lukáš Žídek Research Group

Keywords : carbonic anhydrase, cancer, intrinsically disordered region, NMR, inhibitors


13. Characterization of biomolecules in living cells using NMR spectroscopy

Supervisor : Lukáš Trantírek

RG : Lukáš Trantírek Research Group

Keywords : in-cell NMR spectroscopy; cell-cycle; drug screening; protein


14. The role of the hnRNP C protein in RNA regulation

Supervisor : Jiří Nováček

CF : Cryo-Electron Microscopy and Tomography Core Facility

Keywords : hnRNP C, 40S particle, cryo-EM, cryo-FIBM


Molecular Medicine


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

Supervisor : Dalibor Blažek

RG : Dalibor Blažek Research Group


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

Supervisor: Dalibor Blažek

RG : Dalibor Blažek Research Group


3. PRIORITIZING DRUG COMBINATIONS IN LEUKEMIA BASED ON ANALYSIS OF TARGETTED THERAPY IN VIVO

Supervisor : Marek Mráz

Co-supervisor : Miroslav Boudný

RG : Marek Mráz Research Group


4. LONG NON-CODING RNAs (lncRNAs) IN THE PATHOGENESIS OF B CELL LYMPHOMAS

Supervisor : Marek Mráz

RG : Marek Mráz Research Group


5. The use of CRISPR/Cas9 technology to develop innovative strategies for cellular therapy of hematological malignancies

Supervisor : Michal Šmída

RG : Michal Šmída Research Group


6. The role of posttranscriptional RNA modifications in cell differentiation

Supervisor : Štěpánka Vaňáčová

RGŠtěpánka Vaňáčová Research Group

Keywords:  mRNA, protein interactions, posttranscriptional RNA modifications