Dissertation Topics 2019



Bio-omics


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

Supervisor: Dalibor Blažek, Ph.D.

Consultants: assoc. prof. Zbyněk Zdráhal, Panagiotis Alexiou, Ph.D.

RG: Dalibor Blažek Research Group

Keywords: cyclin-dependent kinases, Cdk12, transcription, recombination repair pathway genes, genome stability, DNA damage, BRCA1, cancer


2. Detailed genomic variant analysis for cancer patient stratification and treatment prognosis

Supervisor: Vojtěch Bystrý, Ph.D.

RG: Šárka Pospíšilová Research Group

Keywords: Next Generation Sequencing, NGS, cancer


3. Development of capillary electrophoresis methods for non-invasive diagnostics of gastroesophageal reflux disease

Supervisor: assoc. prof. Petr Kubáň

Consultant: Ing. František Foret

RG: František Foret Research Group

Keywords: gastroesophageal reflux, GERD, non-invasive samples, capillary electrophoresis, microcolumn separation methods, targeting biomarkers, mass spectrometry


4. Development of portable capillary electrophoresis instrumentation for medical diagnostic purposes

Supervisor: assoc. prof. Petr Kubáň

Consultant: Ing. František Foret

RG: František Foret Research Group

Keywords: non-invasive samples, capillary electrophoresis, microcolumn separation methods, targeting biomarkers, mass spektrometry


5. Developmental response induced by abiotic stress during seed development in Brassica sp.

Supervisor: Helene Robert Boisivon, Ph.D.

RG: Heléne Robert Boisivon Research Group

Keywords: auxin transport, embryonic auxin production, plant reproduction, organogenesis


6. Dynamics of the Structure Maintenance of Chromosome (SMC) complexes

Supervisor: assoc. prof. Jan Paleček

RG: Jiří Fajkus Research Group

Keywords: Structure Maintenance of Chromosome, SMC complexes, SMC5/6; genome stability, chromatin fibers


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

Supervisor: Dalibor Blažek, Ph.D.

Consultant: assoc. prof. Zbyněk Zdráhal, Panagiotis Alexiou, Ph.D.

RG: Dalibor Blažek Research Group

Keywords: cyclin-dependent kinase, Cdk11, transcription, gene expression, cancer


8. Identification of RNA binding protein function and regulation patterns

Supervisor: Panagiotis Alexiou, Ph.D.

RG: Panagiotis Alexiou Research Group

Keywords: Bioinformatics, RNA binding proteins, Machine Learning, Next Generation Sequencing


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

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: Follicular lymphoma, FL, blood cancer, non-Hodgkin lymphoma, B-cell lymphoma, non-coding RNAs, microRNAs, Next Generation Sequencing, NGS, Illumina, genome editing,Crispr, leukemia, DLBCL


10.Mass spectrometric imaging of biological tissues

Supervisor: prof. Jan Preisler

Consultant: Mgr. Markéta Machálková

RG: Jiří Pinkas Research Group

Keywords: mass spectrometry imaging, MSI, matrix-assisted laser desorption/ionization,MALDI, analysis development


11. Mechanisms controlling germ-line differentiation in plants

Supervisor: Karel Říha, Ph.D.

RG: Karel Říha Research Group

Keywords: plant germline, regulation of meiosis


12. Migration of malignant B cells and their adaptive response to BCR inhibitor therapy

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: chronic lymphocytic leukemia, CLL, FCR therapy, NGS technology, BCR signaling inhibitors, genome editing


13. Multistep Phosphorelay Signaling in Crop Stress

Supervisor: assoc. prof. Jan Hejátko

RG: Jan Hejátko Research Group

Keywords: cytokinin regulations, multistep phosphorelay pathway, MSP signal transduction, drought resistence, genome editing, phenotyping, plant hormonal signaling pathways


14. Non-coding RNAs (microRNAS/lncRNAS) and microenvironmental interactions of malignant B-cells

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: B-cell receptor signaling, BCR, leukemia, lymphoma, B cell malignancies, miRNAs, lncRNAs, mRNAs, NGS data analysis, genome editing, Crispr


15. Quality control in diagnostic NGS applications

Supervisor: Boris Tichý, Ph.D.

RG: Core Facility Genomics

Keywords: NGS, diagnostics, whole genome sequencing, exome sequencing, liquid biopsies


16. Regulation of BCR signalling by DNA damage response and P53 protein

Supervisor: assoc. prof. Marek Mráz

RG: Marek Mráz Research Group

Keywords: B-cell receptor, BCR signaling inhibitors, DDR, FOXP1, CD22, chronic lymphocytic leukemia, CLL, NGS technology, genome editing


17. Search for new regulators of intracellular trafficking in plants

Supervisor: Tomasz Nodzynski, Ph.D.

Consultant: Marta Zwiewka, Ph.D.

RG: Tomasz Nodzynski Research Group

Keywords: plants function, intracellular trafficking, endocytic trafficking regulations


18. Structural and functional analysis of cytokinin-regulated DIRIGENT proteins from Arabidopsis thaliana

Supervisor: Blanka Pekárová, Ph.D.

Consultant: assoc. prof. Jan Hejátko

RG: Jan Hejátko Research Group

Keywords: cytokinin regulations, Arabidopsis DIRIGENT proteins,AtDIR13, AtDIR14, plant model Arabidopsis thaliana, hormonal signaling pathways


19. Structure, function and evolution of plant telomere components

Supervisor: prof. Jiří Fajkus

RG: Jiří Fajkus Research Group

Keywords: plant telomere DNA repeats, telomere maintenance, telomerase


20. Syntetic biology in unicellular green algea

Supervisor: Karel Říha, Ph.D.

RG: Karel Říha Research Group

Keywords: picoalgae, genome editing, chromosome segregation


21. Plant signaling at the crossroads of biotic and abiotic interactions

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Martin Černý, Ph.D.

RG: Břetislav Brzobohatý Research Group

Keywords: abiotic stress, biotic stress, multifactorial stress, signaling pathways, transcriptomics, proteomics, metabolomics, lipidomics, hormonomics


22. Cold-light interaction in Arabidopsis cold acclimation: ontogenic and phyllotactic perspective

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Martin Černý, Ph.D.

RG: Břetislav Brzobohatý Research Group

Keywords: cold acclimation, light, frost tolerance, multifactorial stress, signaling pathways, plant hormones, phyllotaxy, ontogenesis, Arabidopsis thaliana, transcriptomics, proteomics, metabolomics, lipidomics


23. The impact of changing environmental conditions on seed germination and early plant development: Omics analyses

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Martin Černý, Ph.D.

RG: Břetislav Brzobohatý Research Group

Keywords: seed germination, plant development, Hordeum vulgare, transcriptomics, proteomics, metabolomics, lipidomics, hormonomics


24. Metabolic regulation of chromatin modifications and gene expression

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Pavel Kerchev, Ph.D.

RG: Břetislav Brzobohatý Research Group

Keywords: plant stress tolerance, genome editing, epigenetics, proteomics, metabolomics, mass spectrometry, LC-MS, GC-MS


25. Abscisic acid – cytokinin crosstalk in regulation of plant development

Supervisor: prof. RNDr. Břetislav Brzobohatý, CSc.

Consultant: Mgr. Jan Novák, Ph.D.

RG: Břetislav Brzobohatý Research Group

Keywords: abscisic acid, cytokinin, plant development, transcriptomics, proteomics, metabolomics, lipidomics



Structural Biology


1. A structural basis for the cross-talk between histones and RNA Polymerase II

Supervisor:  assoc. prof. Richard Štefl

Consultants: Karel Kubíček, PhD., assoc. prof. Štěpánka Vaňáčová

RG: Richard Štefl Research Group

Keywords: RNA, posttranslational modifications, CTD, RNAPII, histones, chromatin, C-terminal domain, gene expression


2.  Characterizing sequence-structure-function relationships: A multi-dimensional approach for evaluating similarity in structural biology data

Supervisor: prof. Jaroslav Koča

Consultants: Crina-Maria Ionescu, Ph.D.

RG: Jaroslav Koča Research Group

Keywords: biomolecules, sequence-structure-function relationship, data analysis


3. Cracking the CTD code

Supervisor: assoc. prof. Richard Štefl

Consultants: Karel Kubíček, PhD., Pavel Plevka, Ph.D.

RG: Richard Štefl Research Group

Keywords: CTD, TNAPII, C-terminal domain, CTD code, post-translational modification


4. Designing modified DNA fragments

Supervisor: prof. Radek Marek

RG: Radek Marek Research Group

Keywords: modified DNA quadruplexes, NMR spectroscopy, structure and biophysical properties


5. Experimental and Theoretical Studies of the Origin of Life on the Earth

Supervisor: prof. Jiří Šponer

Consultants: Judit Šponerová, PhD.

RG: Jiří Šponer Research Group

Keywords: oligonucleotide sequences, quantum chemistry and molecular dynamics simulations, abiogenesis of RNA, QM methods, catalytic activity of RNA, MD simulations


6. Impact of 14-3-3 protein on the formation of protein aggregates involved in neurodegenerative diseases

Supervisor: Jozef Hritz, Ph.D.

Consultants: assoc. prof. Vítězslav Bryja, Jan Přibyl, Ph.D.

RG: Lukáš Žídek Research Group

Keywords: tau and Abeta protein, post-translational modifications, phosphorylation, 14-3-3 proteins, atomic force microscopy, neurodegenerative diseases, AFM


7. Influence of membrane properties on peptide conformations

Supervisor: assoc. prof. Robert Vácha

RG: Robert Vácha Research Group

Keywords: protein conformations, phospholipid membrane, neurodegenerative peptides, Alzheimer’s disease, Abeta peptide, peptide conformations, membrane parameterizations


8. Integrative structural biology of 3’UTRs

Supervisor: Peter Lukavsky, Dr. rer. nat.

Consultants: Boris Tichý, Ph.D., assoc. prof. Zbyněk Zdráhal

RG: Peter Lukavsky Research Group

Keywords: Three Prime Untranslated Region, 3’UTR, mRNPs, RNA-protein networks, Staufen, RNA-based pulldown, gene expression, 3’UTR mutations, cryo EM, NMR spectroscopy


9. Interaction of selected phosphor-peptides and organic molecules with 14-3-3 proteins 

Supervisor: Jozef Hritz, Ph.D.

Consultants: prof. Lukas Žídek

RG: Lukáš Žídek Research Group

Keywords: neurodegenerative diseases, Alzheimer disease, protein fibrils, phosphorylation state, 14-3-3 proteins, cryoEM tomography, NMR


10.Interactions underlying physiological function of Microtubule Associated Protein 2c

Supervisor: prof. Lukáš Žídek,

Consultants: Jozef Hritz, Ph.D.

RG: Lukáš Žídek Research Group

Keywords: Microtubule Associated Protein 2c, MAP2c, NMR spectroscopy, cryo-electron tomography, 14-3-3 protein


11. Multiscale Modeling of Nucleic Acids

Supervisor: prof. Jiří Šponer

Consultants: prof. Michal Otyepka, Judit Šponerová, PhD

RG: Jiří Šponer Research Group

Keywords: nucleic acids, multiscale modeling, QM, MD methods, protein-RNA complexes, RNA catalysis, quadruplex DNA


12. New methods in NMR structure determination to facilitate structural studies of macromolecular complexes

Supervisor: Konstantinos Tripsianes, Ph.D.

RG: Konstantinos Tripsianes Research Group

Keywords: structure determination, next-generation NMR, NOESY, DNA repair, transcription


13. Protein sensitivity of membrane curvature

Supervisor: assoc. prof. Robert Vácha

RG: Robert Vácha Research Group

Keywords: membrane curvature, protein sequencing, protein motifs design, membrane parameterizations


14. Regulation of protein-protein itneractions

Supervisor: assoc. prof. Robert Vácha

RG: Robert Vácha Research Group

Keywords: protein interactions, posttranslational modifications, multi-scale simulations, protein motifs design, protein parameterization


15. Structural basis of function of receiver domains of plant hybrid histidine kinases

Supervisor: prof. Lukáš Žídek

Consultants: Jozef Hritz, Ph.D., assoc. prof. Jan Hejátko

RG: Lukáš Žídek Research Group

Keywords: hybrid histidine kinase, CKI1, Arabidopsis thaliana, NMR, conformational changes


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

Supervisor: Pavel Plevka, Ph.D.

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


17. Structural changes of the selected protein fibrils induced by phosphorylation and the interaction with 14-3-3 proteins

Supervisor: Jozef Hritz, Ph.D.

Consultant: assoc. prof. Vítězslav Bryja

RG: Lukáš Žídek Research Group

Keywords: neurodegenerative diseases, Alzheimer disease, protein fibrils, phosphorylation state, 14-3-3 proteins, cryoEM tomography, NMR


18. Structural characterization of nucleic acid modifying enzymes

Supervisor: prof. Mary Anne O'Connell

Consultant: Liam Keegan, Ph.D., Jiří Nováček, Ph.D.

RG: ERA Chair - Mary O'Connell Research Group

Keywords: RNA modifications, epitranscriptome, liquid chromatography-mass spektrometry, LC-MS, Poly(A) RNA, miRNA


19. Structural study of enterovirus replication in vivo

Supervisor: Pavel Plevka, Ph.D.

RG: Pavel Plevka Research Group

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


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

Supervisor: prof. Radek Marek

Consultant: Jan Novotný, Ph.D.

RG: Radek Marek Research Group

Keywords: oligonucleotides, MD simulations, molecular modelling, NMR spectroscopy


21. Structure, dynamics and interactions of subunits of RNA polymerase of Gram-positive bacteria

Supervisor: prof. Lukáš Žídek

Consultant: Pavel Kadeřávek, Ph.D.

RG: Lukáš Žídek Research Group

Keywords: Gram-positive bacteria, RNA polymerase subunits, NMR spectroscopy, X-ray crystallography, cryo-electron microscopy


22. Structural biology of ion channels

Supervisor: prof. Jaroslav Koča

Consultant: Crina-Maria Ionescu, Ph.D.

RG: Jaroslav Koča Research Group

Keywords: biomolecule, membrane protein, bioinformatics


23. Structure-functional study of proteins involved in host cell recognition

Supervisor: prof. RNDr. Michaela Wimmerová, Ph.D.

RG: Michaela Wimmerová Research Group

Keywords: lectins, pathogens, X-ray crystallography, biomolecular interactions, tissue specific glycosylation