Dissertation topics - 2018



Bio-omics

1.Application of modern microcolumn separation methods coupled to mass spectrometry for analysis of non-invasive biological samples
Supervisor : doc. RNDr. Petr Kubáň, Ph.D.
Consultant : Ing. František Foret, CSc.
RG: František Foret Research Group
Keywords : non-invasive samples, microcolumn separation methods, targeting biomarkers, mass spectrometry

2. DIRIGENT Genes in the Control of Plant Development
Supervisor : doc. RNDr. Jan Hejátko, Ph.D.
RG: Jan Hejátko Research Group
Keywords : cytokinins, CKs, multistep phosphorelay signaling, MSP, AtDIR, Brillouin imaging, plant hormonal signaling pathways, mdel plant Arabidopsis thaliana

3. Discovery of genes governing differentiation of plant germline
Supervisor : Mgr. Karel Říha, Ph.D.
RG: Karel Říha Research Group
Keywords : plant germline

4. Genetic variability in multistep phoshorelay signaling in plants
Supervisor : doc. RNDr. Jan Hejátko, Ph.D.
RG: Jan Hejátko Research Group
Keywords : cytokinins, multistep phosphorelay signaling, MSP, cytokinin receptors, plant phenotyping,  biotic and abiotic stresses

5. Genome evolution in the Brassicales
Supervisor : doc. Mgr. Martin Lysák, Ph.D.
RG: Martin Lysák Research Group
Keywords : Brassicales, evolutionary biology, phylogenomic tools

6. Characterization of Cdk12 and Cdk13 kinase substrates and their role in development of cancer
Supervisor : Mgr. Dalibor Blažek, Ph.D.
Consultant : doc. RNDr. Zbyněk Zdráhal, Dr.
RG: Dalibor Blažek Research Group
Keywords : cyclin-dependent kinases, Cdk12, Cdk13, recombination repair pathway genes, BRCA1, cancer

7. Identification of novel therapies for genetically defined CLL cases through repurposing of already approved drugs
Supervisor : Mgr. Michal Šmída, Dr. rer. nat.
Consultant : prof. RNDr. Šárka Pospíšilová, Ph.D.
RG: Michal Šmída Research Group
Keywords : B-cell chronic lymphocytic leukemia,CLL therapy, selective drugs, drug repurposing

8. Light-responsive proteins and their role in plant development
Supervisor : prof. RNDr. Břetislav Brzobohatý, CSc.
Consultant : Mgr. Martin Černý, Ph.D.
Annotation : Light represents a key factor influencing plants. Light quality and quantity influence all major developmental transitions such as seed germination or flowering. The main objective of this thesis is to analyse proteome of model plants Arabidopsis thaliana and Solanum lycopersicum and identify light-responsive proteins. The effects of the light quality (spectral composition), intensity and the light period duration will be compared. Dedicated adjustable LED light-equipped growth chambers will be used to follow changes in (i) seedlings transferred from optimal to sub-optimal light conditions, and (ii) effects of prolonged growth at modulated light conditions. An LC-MS label-free proteome profiling will be used to identify key light responsive proteins. These proteins will be targeted in consecutive analyses via an SRM-based analysis which will allow a high-throughput screening in multiple samples. The proteomic experiments will be supplemented and validated by complementary techniques (e.g. morphometric analysis, microscopy, RT-qPCR). Based on the results and in collaboration with her supervisor and co-supervisor, the student will design additional experiments to bring insight into the nature of light signaling.
Keywords : light-responsive proteins, LC-MS label-free proteome profiling, SRM-based analysis, RT-qPCR, light signaling, model plant Arabidopsis thaliana and Solanum lycopersicum

9. Mass spectrometric imaging of biological tissues
Supervisor : prof. Mgr. Jan Preisler, Ph.D.
Consultant : Mgr. Markéta Machálková
RG: Jiří Pinkas Research Group
Keywords : mass spectrometry imaging, MSI, matrix-assisted laser desorption/ionization,MALDI, analysis development

10. Non-Coding RNAS and Microenvironmental Interactions of B-Cell Leukemias and Lymphomas
Supervisor : doc. MUDr. Mgr. Marek Mráz, Ph.D.
RG: Marek Mráz Research Group
Keywords : microenvironmental interactions, B-cell receptor signaling, BCR, non-coding RNAs, microRNA, genome editing, NGS data analysis, leukemia, lymphoma

11. Repeatome evolution in crucifers
Supervisor : doc. Mgr. Martin Lysák, Ph.D., DSc.
RG: Martin Lysák Research Group
Keywords : crucifer genomes, next-generation sequencing, phylogenetic, repeatome evolution

12. Role of Cdk12 in regulation of gene expression/DNA damage response in ovarian cancer
Supervisor : Mgr. Dalibor Blažek, Ph.D.
Consultant : doc. RNDr. Zbyněk Zdráhal, Dr.
RG: Dalibor Blažek Research Group
Keywords : cyclin-dependent kinase 12, Cdk12, regulation of gene expression, ovarian carcinoma, DNA damage response, mass spektrometry, next generation sequencing

13. SMC complexes dynamics
Supervisor : doc. Mgr. Jan Paleček, Dr. rer. nat.
RG: Jiří Fajkus Research Group
Keywords : Structure Maintenance of Chromosome, SMC complexes, SMC5/6; genome stability, chromatin fibers

14.Structural and functional analysis of cytokinin-regulated DIRIGENT proteins from Arabidopsis thaliana
Supervisor : Ing. Blanka Pekárová, Ph.D.
Consultant : doc. RNDr. Jan Hejátko, Ph.D.
RG: Jan Hejátko Research Group
Keywords : cytokinin regulations, Arabidopsis DIRIGENT proteins,AtDIR13, AtDIR14, plant model Arabidopsis thaliana, hormonal signaling pathways

15. Structure, function and evolution of plant telomere components
Supervisor : prof. RNDr. Jiří Fajkus, CSc.
RG: Jiří Fajkus Research Group
Keywords : plant telomere DNA repeats, telomere maintenance, telomerase

16. The mechanisms of drug resistance and adaptive response in chronic lymphocytic leukemia
Supervisor : doc. MUDr. Mgr. Marek Mráz, Ph.D.
RG: Marek Mráz Research Group
Keywords : chronic lymphocytic leukemia, CLL, FCR therapy, NGS technology, therapy resistence, BCR signaling inhibitors, genome editing

17. The role of cytokinin-inducible EXPANSINs in the control of cell wall properties and development in Arabidopsis
Supervisor : Mgr. Markéta Šámalová, Ph.D.
Consultant : doc. RNDr. Jan Hejátko, Ph.D.
RG: Jan Hejátko Research Group
Keywords : CK-regulated genes, EXPANSINs, cell wall properties control, CRISPR-Cas9 gene-editing, Brillouin imaging

18. The role of cytokinins in determination of organ identity
Supervisor : Mgr. Markéta Pernisová, Ph.D.
Consultants : prof. RNDr. Jiří Fajkus, CSc., Helene Robert Boisivon, Ph.D.
RG: Jiří Fajkus Research Group
Keywords : cytokinin signalling, plant organogenesis, organ identity

19. The role of non-coding RNAs in the pathogenesis of aggressive follicular lymphoma and its high-grade transformation
Supervisor : doc. MUDr. Mgr. Marek Mráz, Ph.D.
RG: Marek Mráz Research Group
Keywords : Follicular lymphoma, FL, blood cancer, non-Hodgkin lymphoma, B-cell lymphoma, non-coding RNAs, microRNAs, Next Generation Sequencing, Illumina, genome editing,Crispr

20. Transcriptional regulation of auxin-dependent organogenesis
Supervisor : Helene Robert Boisivon, Ph.D.
Consultants : Mgr. Markéta Pernisová, Ph.D.
RG: Heléne Robert Boisivon Research Group
Keywords : auxin transport, embryonic auxin production, plant reproduction, organogenesis

21. Mechanisms controlling germ-line differentiation in plants
Supervisor: Mgr. Karel Říha, Ph.D.
RG: Karel Říha Research Group
Keywords : plant germline

22. Analysis of genomic data in patients with chronic lymphocytic leukemia
Supervisor: Mgr. Karla Plevová, Ph.D.
RG: Šárka Pospíšilová Research Group
Keywords: chronic lymphocytic leukemia, cancer genome, clonal evolution, biomarkers, mutation signature, expression pattern, tumor interactions, bioinformatics tools, computing technologies

23. 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


Structural Biology

1. A structural basis for the cross-talk between histones and RNA Polymerase II
Supervisor : doc. Mgr. Richard Štefl, Ph.D.
Consultants : Mgr. Karel Kubíček, PhD., doc. Mgr. Štěpánka Vaňáčová, Ph.D.
RG: Richard Štefl Reserch Group
Keywords : RNA, posttranslational modifications, CTD, RNAPII, histones, chromatin, C-terminal domain, gene expression

2. Atomic resolution study of transient structures and complexes of Microtubule Associated Protein 2c
Supervisor : prof. Mgr. Lukáš Žídek, Ph.D.
Consultants : RNDr. Mgr. Jozef Hritz, Ph.D.
RG: Lukáš Žídek Research Group
Keywords : Microtubule Associated Protein 2c, MAP2c, NMR spectroscopy, X-ray crystallography, transient structures, nerve cells

3. Behavior of alternative DNA structures at electrically charged surfaces
Supervisor : doc. RNDr. Miroslav Fojta, CSc.
RG: Miroslav Fojta Research Group
Keywords : DNA structures, DNA conformation, guanine quadruplexes, oligonucleotides, electrochemical techniques

4. Cracking the CTD code
Supervisor : doc. Mgr. Richard Štefl, Ph.D.
Consultants : Mgr. Karel Kubíček, PhD., Mgr. Pavel Plevka, Ph.D.
RG: Richard Štefl Reserch Group
Keywords : CTD, TNAPII, C-terminal domain, CTD code, post-translational modification

5. Cryo-electron microscopy analysis of influenza A replication in vivo
Supervisor : Mgr. Pavel Plevka, Ph.D.,
RG: Pavel Plevka Research Group
Keywords : Influenza A virus, replication cycle, cryo-electron microscopy, cryo-electron tomography

6. Designing modified DNA fragments
Supervisor : prof. RNDr. Radek Marek, Ph.D.
RG: Radek Marek Research Group
Keywords : modified DNA quadruplexes, NMR spectroscopy, structure and biophysical properties

7. Development and evaluation of next-generation drug design algorithms
Supervisor : Konstantinos Tripsianes, Ph.D.
Consultants : doc. RNDr. Tomáš Brázdil, Ph.D., Thomas Evangelidis, M.Phil., Ph.D.
RG: Konstantinos Tripsianes Research Group
Keywords : ScaffOpt, Metapredictor, binding affinity, virtual screening, ligand-based drug design, docking, Python programming, next-generation drug design, next-generation drug

8. Engineering the glycans of stem cells to have required bioactivity – a computational study combined with an experiment
Supervisor : prof. RNDr. Jaroslav Koča, DrSc.
Consultants : Ing. Igor Tvaroška, DrSc.
RG: Jaroslav Koča Research Group
Keywords : chemoattractants, alpha(1,3)-fucosylation, ligands selection, glycans

9. Experimental and Theoretical Studies of the Origin of Life on the Earth
Supervisor : prof. RND. Jiří Šponer, DrSc.
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

10. Impact of 14-3-3 protein on the formation of protein aggregates involved in neurodegenerative diseases
Supervisor : RNDr. Mgr. Jozef Hritz, Ph.D.
Consultants : doc. Mgr. Vítězslav Bryja, Ph.D., Mgr. 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

11.Influence of membrane properties on peptide conformations
Supervisor : doc. RNDr. Robert Vácha, PhD.
RG: Robert Vácha Research Group
Keywords : protein conformations, phospholipid membrane, neurodegenerative peptides, Alzheimer’s disease, Abeta peptide, peptide conformations, membrane parameterizations

12. Multiscale Modeling of Nucleic Acids
Supervisor : prof. RNDr. Jiří Šponer, DrSc.
Consultants: prof. RNDr. Michal Otyepka, Ph.D., Judit Šponerová, PhD
RG: Jiří Šponer Research Group
Keywords : nucleic acids, multiscale modeling, QM, MD methods, protein-RNA complexes, RNA catalysis, quadruplex DNA

13. Partial atomic charges – a clue to predict chemical and biological behaviour of biomacromolecules
Supervisor : prof. RNDr. Jaroslav Koča, DrSc.
RG: Jaroslav Koča Research Group
Keywords : biomacromolecules, partial atomic charges, data analysis

14. Protein sensitivity of membrane curvature
Supervisor : doc. RNDr. Robert Vácha, PhD.
RG: Robert Vácha Research Group
Keywords : membrane curvature, protein sequencing, protein motifs design, membrane parameterizations

15. Structural basis of function of receiver domains of plant hybrid histidine kinases
Supervisor : prof. Mgr. Lukáš Žídek, Ph.D.
Consultants : RNDr. Mgr. Jozef Hritz, Ph.D., doc. RNDr. Jan Hejátko, Ph.D.
RG: Lukáš Žídek Research Group
Keywords : hybrid histidine kinase, CKI1, Arabidopsis thaliana, NMR, conformational changes

16. Structural changes of the selected protein fibrils induced by phosphorylation and the interaction with 14-3-3 proteins
Supervisor : RNDr. Mgr. Jozef Hritz, Ph.D.
Consultants : doc. Mgr. Vítězslav Bryja, Ph.D., Dr. Tanvir Shaikh
RG: Lukáš Žídek Research Group
Keywords : neurodegenerative diseases, Alzheimer disease, protein fibrils, phosphorylation state, 14-3-3 proteins, cryoEM tomography, NMR

17. Structure, dynamics and interactions of subunits of RNA polymerase of Gram-positive bacteria
Supervisor : prof. Mgr. Lukáš Žídek, Ph.D.
Consultants : Mgr. Pavel Kadeřávek, Ph.D.
RG: Lukáš Žídek Research Group
Keywords : Gram-positive bacteria, RNA polymerase subunits, NMR spectroscopy, X-ray crystallography, cryo-electron microscopy

18. 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

19. The Three Prime Untranslated Region (3'UTR)
Supervisor : Mgr. PharmDr. Peter Lukavsky, Dr. rer. nat.
Consultants : MVDr. Boris Tichý, Ph.D., doc. RNDr. Zbyněk Zdráhal, Dr.
RG: Peter Lukavsky Research Group
Keywords : Three Prime Untranslated Region, 3’UTR, mRNPs, RNA-protein networks, CaMKIIa, SHAPE sequencing, RNA-based pulldown, gene expression, 3’UTR mutations

20. Characterizing sequence-structure-function rela-tionship: A multi-dimensional approach for evaluating similarity in structural biology data
Supervisor : prof. RNDr. Jaroslav Koča, DrSc.
Consultants : Mgr. Ing. Crina-Maria Ionescu, Ph.D.
RG: Jaroslav Koča Research Group
Keywords : biomolecules, sequence-structure-function relationship, data analysis

21. Interaction of selected phosphor-peptides and organic molecules with 14-3-3 proteins
Supervisor: RNDr. Mgr. Jozef Hritz, Ph.D.
Consultants: Prof. Mgr. Lukas Zidek, Ph.D.

RG: Lukáš Žídek Research Group
Keywords: neurodegenerative diseases, Alzheimer disease, protein fibrils, phosphorylation state, 14-3-3 proteins, cryoEM tomography, NMR