Vědy o živé přírodě

Ribosome-associated quality control (RQC) is crucial for degrading truncated nascent proteins produced on aberrant mRNAs. Mutations in RQC components cause neurodegeneration both in animal models and human patients. Moreover, RQC insufficiency and subsequent protein aggregation critically contribute to proteostasis impairment and systemic decline during ageing. The successful candidate will utilize a multidisciplinary approach to provide detailed mechanistic understanding of the critical human RQC system in combination with an in vivo study to reveal processes leading to RQC-driven pathological changes in neural tissue. He/she will utilize human cell cultures, protein expression and purification techniques and biochemistry methods to produce samples for cryogenic electron microscopy (cryo-EM). Comprehensive training in cryo-EM will be available to the successful candidate. The candidate will also have a unique opportunity to acquire expertise in the use of C. elegans as a model organism during a research stay at a collaborating laboratory in Bolzano (Italy).

Requirements on candidates:

The ideal candidate should have a background in either molecular biology, biochemistry, or structural biology. Experience with human cell culture work or protein biochemistry is a plus.

More information: RG Translation Control

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link)

 

Poznámky

Recommended literature:

Tesina, P., et al., Molecular basis of eIF5A-dependent CAT tailing in eukaryotic ribosome-associated quality control. Mol Cell, 2023. 83(4): p. 607-621 e4.

Lu, B., Translational regulation by ribosome-associated quality control in neurodegenerative disease, cancer, and viral infection. Front Cell Dev Biol, 2022. 10: p. 970654.

Filbeck, S., et al., Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell, 2022. 82(8): p. 1451-1466.

Udagawa, T., et al., Failure to Degrade CAT-Tailed Proteins Disrupts Neuronal Morphogenesis and Cell Survival. Cell Rep, 2021. 34(1): p. 108599.

Aviner, R., et al., Ribotoxic collisions on CAG expansions disrupt proteostasis and stress responses in Huntington’s Disease. bioRxiv, 2022: p. 2022.05.04.490528.

Školitel

RNDr. Petr Těšina, Ph.D.

This PhD theme focuses on unraveling the intricate process of Argonaute protein loading by small RNAs, a
critical step in gene regulation within RNA-silencing pathways, which are pivotal in both healthy and diseased
states of animals and plants. Despite over two decades of research into the microRNA pathway and RNA
interference, the precise mechanisms of miRNA strand selection and transfer to Argonaute proteins remain
elusive. We propose the existence of two distinct mammalian Argonaute loading pathways, orchestrated by
Dicer and heat shock protein chaperones, which both involve charged intrinsically disordered regions that
have been overlooked in previous structural studies. The PhD project aims to dissect these mechanisms
using electron cryomicroscopy (cryoEM). The objective is to elucidate the structures of critical complexes
involving heat shock protein chaperone/co-chaperone-Argonaute-RNA and Dicer-Argonaute-RNA
assemblies. By integrating cryoEM with functional analyses, the project aspires to establish the mechanistic
principles of Argonaute loading. The findings of this PhD project will be instrumental in advancing RNAbased
therapeutic applications and understanding one of the most crucial regulatory cellular processes.

Requirements on candidates:

Biochemistry/molecular biology

More information: RG Structural Biology of Gene Regulation

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1) Dicer structure and function: conserved and evolving features. Zapletal D, Kubicek, K, Svoboda P, Stefl R EMBO Reports (2023) 24:e57215 doi:10.15252/embr.202357215

2) microRNAs in action: biogenesis, function and regulation. Shang R, Lee S, Senavirathne G, Lai EC. Nat Rev Genet. 2023 doi:10.1038/s41576-023-00611-y.

Školitel

prof. Mgr. Richard Štefl, Ph.D.

Membrane fusion is an essential biological process that plays a crucial role in neurotransmission,
intracellular trafficking, and immune responses. Despite its fundamental biological role and
potential application in drug delivery, the molecular understanding of membrane fusion and its
control remain elusive. This project is focused on the design of novel peptides and peptide
aggregates able to induce spontaneous fusion. The peptides have been selected based on their
biocompatibility and our exceptional experience with membrane-active peptides, including the
design of de novo sequences based on the elucidated mechanism. The first step will be to develop
a computational approach to determine the critical peptide properties required to destabilize or
stabilize key fusion states: membrane stalk, hemifusion diaphragm, and fusion pore. These
findings will then be used to de novo design peptide sequences where the fusogenic role of each
amino acid is known, providing the key advantage for customization for vaccination and drug
delivery. The computational results will be verified by fluorescence and electron microscopy.

Requirements on candidates:

Outstanding candidates with experience in computer simulations and with an MSc/PhD degree in
the fields of biophysics, soft matter physics, physical chemistry, computational chemistry,
statistical mechanics, or related fields. Experience with molecular dynamics simulations (with
GROMACS, CHARMM, NAMD, AMBER, LAMMPS, etc.) at the atomistic or coarse-grained level
would be an advantage.

More information: RG Interaction Protein-Protein and Protein-Membrane

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

 

Poznámky

Recommended literature:

Biophys J 2022, 121, 852–861, doi: 10.1016/j.bpj.2021.12.035

Nat Rev Mol Cell Biol 2024, 25(2), 101-118, doi: 10.1038/s41580-023-00668-x

PNAS 2014, 111 (30), 11043-11048, doi: 10.1073/pnas.1323221111

Školitel

prof. RNDr. Robert Vácha, PhD.

Novel forms of nucleotides will be incorporated in silico in oligomers with sequences relevant for biosystems. The biocompatibility of artificial building blocks will be evaluated using advanced methods of quantum chemistry (that provide also analytical tools for investigation of crucial noncovalent interactions) and molecular dynamics. Available candidates of modified nucleobases and sugars will be investigated experimentally by using NMR spectroscopy in solution.

Requirements on candidates:

Computational and quantum chemistry, structural chemistry or biology.

More information: RG Structure of Biosystems and Molecular Materials

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

 

Poznámky

Recommended literature:

CUYACOT, Ben J.R., Ivo DURNÍK, Cina FOROUTAN-NEJAD and Radek MAREK. Anatomy of Base Pairing in DNA by Interacting Quantum Atoms, Journal of Chemical Information and Modeling, 2021, 61, 211-222. doi:10.1021/acs.jcim.0c00642.

YURENKO, Yevgen, Jan NOVOTNÝ and Radek MAREK. Weak Supramolecular Interactions Governing Parallel and Antiparallel DNA Quadruplexes: Insights from Large-Scale Quantum Mechanics Analysis of Experimentally Derived Models. Chemistry - A European Journal, 2017, 23, 5573-5584. doi:10.1002/chem.201700236.

DUREC, Matúš, Francesco ZACCARIA, Célia FONSECA GUERRA and Radek MAREK. Modified guanines as constituents of smart ligands for nucleic acid quadruplexes. Chemistry - A European Journal, 2016, 22, 10912-10922. doi:10.1002/chem.201601608.

BAZZI, Sophia, Jan NOVOTNÝ, Yevgen YURENKO and Radek MAREK. Designing a New Class of Bases for Nucleic Acid Quadruplexes and Quadruplex-Active Ligands. Chemistry - A European Journal, 2015, 21, 9414-9425. doi:10.1002/chem.201500743.

YURENKO, Yevgen, Jan NOVOTNÝ, Vladimír SKLENÁŘ and Radek MAREK. Substituting CF2 for O4' in Components of Nucleic Acids: Towards Systems with Reduced Propensity to Form Abasic Lesions. Chemistry - A European Journal, 2015, 21, 17933-17943. doi:10.1002/chem.201502977.

Školitel

prof. RNDr. Radek Marek, Ph.D.

Dishevelled (DVL) is the central hub of Wnt signal transduction that integrates and transduces upstream signals through distinct cytoplasmic cascades. Looking at the many DVL faces reported in literature, three salient features underlying its function in signaling can be highlighted: (1) it interacts with more than seventy binding partners, (2) it is heavily phosphorylated at multiple sites by at least eight different kinases, in particular by Ck1epsilon/sigma after Wnt stimulation, and (3) it consistently forms puncta in the cytosol, that are phase-separated self-assemblies also called liquid droplets.
Our working hypothesis is that DVL conformational plasticity mediated by the order-disorder interactions allows the combinatorial integration of phosphorylation input, partners binding, self assembly in droplets, and allosteric coupling, to exquisitely control signal routing. We integrate structural biology (NMR, SAXS, X-ray, MS-HDX) and biophysical techniques (FRET, ITC, BLI) with cellular readouts (TopFlash, BRET) to understand DVL structure, function, and regulation. Candidates can choose among three open questions, that if resolved, will have significant impact on Wnt research.
1) Does disorder provide new contexts to structured domain(s) and, hence, enhance the DVL functional space associated with them?
2) Is there a direction, order or hierarchy in the phosphorylation of individual S/T sites and clusters in DVL?
3) What are the physical behaviors associated with intrinsic disorder and their connection to DVL liquid-liquid phase separation?

Requirements on candidates:

Biomolecular NMR, Biochemistry, Molecular Cell Biology

More information: RG Protein-DNA Interactions

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

Kravec M. et al. A new mechanism of posttranslational polyglutamylation regulates phase separation and signaling of the Wnt pathway protein Dishevelled. Embo J., 2024 (accepted)

Hanáková K. et al. Comparative phosphorylation map of Dishevelled 3 links phospho-signatures to biological outputs. Cell Commun. Signal., 2019. 17: p. 170

Harnoš J. et al. Dishevelled-3 conformation dynamics analyzed by FRET-based biosensors reveals a key role of casein kinase 1. Nat. Commun., 2019. 10: p. 1804

Školitel

Konstantinos Tripsianes, Ph.D.

Eukaryotic and prokaryotic plasma membranes exhibit inherent asymmetry, with distinct lipid
compositions between the two leaflets. However, most studies to date have focused on symmetric
bilayers. This project addresses this gap by integrating molecular dynamics simulations with
experimental techniques such as solid-state NMR spectroscopy and scattering methods. The
primary aim is to elucidate the structural and dynamical properties of lipids in asymmetric
membranes, particularly their interactions with integral membrane proteins, with an emphasis on
bacterial lipid compositions. Initial step will involve determining lipid chain order parameters,
bilayer structure, and lipid dynamics. Subsequently, lipid-protein interactions will be assessed,
focusing on lipid-induced modulation of enzymatic activity in two bacterial proteins: OmpLA, a beta-
barrel protein, and GlpG, an alpha-helical transmembrane protein. The findings will offer key insights
into the role of lipid asymmetry in biological membranes and its influence on membrane protein
function, with potential applications in the development of lipid-targeted therapeutics and
biosensors for pharmaceutical and biotechnological use.

Requirements on candidates:

Outstanding candidates with experience in computer simulations and with an MSc/PhD degree in
the fields of biophysics, soft matter physics, physical chemistry, computational chemistry,
statistical mechanics, or related fields. Experience with molecular dynamics simulations (with
GROMACS, CHARMM, NAMD, AMBER, LAMMPS, etc.) at the atomistic or coarse-grained level
would be an advantage.

More information: RG Interaction Protein-Protein and Protein-Membrane

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Bartoš, L., Vácha, R.: Biophys. J. 2024, 123, 1-10

2. M. Bogdanov, K. Pyrshev, S. Yesylevskyy, S., Ryabichko, V. Boiko, P. Ivanchenko, R. Kiyamova, Z. Q. Guan, C. Ramseyer, W. Dowhan, Sci. Adv. 2020, 6.

3. G. J. Schutz, G. Pabst, Bioessays 2023, e2300116

4. M. Varma, M. Deserno, Biophys. J. 2022, 121, 4001-4018

Školitel

prof. RNDr. Robert Vácha, PhD.

The main neuropathological signs of Alzheimer’s disease are associated with the
fibrillization of tau protein into neurofibrillary tangles. Studying how different factors
influence the formation of protein fibrils is the key to understanding these
neurodegenerative processes. The main aim of this PhD project will be the
characterization of conformational changes towards the formation of tau fibrils due to
their truncations, phosphorylation, and interaction with 14-3-3 proteins. An
interdisciplinary approach combining biomolecular NMR, biophysical interaction
techniques, and computational methods will be applied. Special emphasis will be used
for the applying of solution NMR spectroscopy for the monitoring of secondary structure
propensities and proline conformations within Tau and alpha-synuclein protein as well as
binding epitopes of their selected binding partners.

Requirements on candidates:

Preferable candidate’s background in biophysics/biophysical chemistry, biochemistry, structural or molecular biology.

More information: RG Protein Structure and Dynamics

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Kitoka K, Lends A, Kučinskas G, Bula AL, Krasauskas L, Smirnovas V, Zilkova M; Kovacech B, Skrabana R, Hritz J, Jaudzems K*: dGAE(297-391) tau fragment promotes the formation of CTE-like full-length tau filaments, Angew. Chem. Int. Ed. 2024, e202407821.

2. Crha R., Kozeleková A., Hofrová A., Iľkovičová L., Gašparik N., Kadeřávek P., Hritz J.*: Hiding in plain sight: Complex interaction patterns between Tau and 14-3-3 zeta protein variants. Int. J. Biol. Macromol. 2024, 266, 130802.

3. Lasorsa A., Bera K., Malki I., Dupré E., Cantrelle F., Merzougui H., Sinnaeve D., Hanoulle X., Hritz J.*, Landrieu I.*: Conformational impact of multiple phosphorylations within BIN1 SH3 domain binding site in the proline rich region of Tau protein. Biochemistry 2023, 62, 1631–1642, doi: 10.1021/acs.biochem.2c00717.

4. Trosanova Z., Lousa P., Kozelekova A., Brom T., Gasparik N., Tungli J., Weisova V., Zupa E., Zoldak G., Hritz J.*: Quantitation of human 14-3-3 zeta dimerization and the effect of phosphorylation on dimer-monomer ekvilibria. J. Mol. Biol. 2022, 434, 167479.

5. Zapletal, V.; Mládek, A.; Melková, K.; Louša, P.; Nomilner, E.; Jaseňáková, Z.; Kubáň, V.; Makovická, M.; Laníková, A.; Žídek L.; Hritz, J.* Choice of force field for proteins containing structured and intrinsically disordered regions. Biophys. J. 2020, 118, 1621 – 1633.

6. Louša, P.; Nedozrálová, H.; Župa, E.; Nováček, J.; Hritz, J.*: Phosphorylation of the regulatory domain of human tyrosine hydroxylase 1 monitored using non-uniformly sampled NMR. Biophys. Chem. 2017, 223, 25-29.

7. Jansen S., Melková K., Trošanová Z., Hanáková K., Zachrdla M., Nováček J., Župa E., Zdráhal Z., Hritz J.*, Žídek L.*: Quantitative Mapping of MAP2c Phosphorylation and 14-3-3zeta Binding Sites Reveals Key Differences Between MAP2c and Tau. J. Biol. Chem. 2017, 292, 6715-6727.

Školitel

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

To initiate infection, viruses deliver their genomes into host cells. Whereas enveloped viruses fuse their
membrane with that of a cell, the cell entry mechanisms employed by non-enveloped viruses are less
understood. Recently, it has been shown that endosome rupture enables cell entry of picornaviruses. The
student will analyze the putative role of endosome rupture in the cell entry of adenoviruses, polyomaviruses,
and parvoviruses. He/She will employ cryo-electron microscopy and tomography to visualize the early stages
of cell virus entry in peripheral parts of cells that can be imaged using transmission electron microscopy.
The student will analyze changes in the structure of virus particles and endosome membranes that enable
the viruses to deliver their genomes into the cytoplasm.

Requirements on candidates:

The prospective student should be interested in learning cryo-EM and structure determination approaches.
Previous experience with molecular biology, programming, scripting, and data analyses is a plus.

More information: RG Structural Virology

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Virus entry by endocytosis. Mercer J, Schelhaas M, Helenius A. Annu Rev Biochem. 2010;79:803-33. doi: 10.1146/annurev-biochem-060208-104626. PMID: 20196649

2. Adenovirus Entry: From Infection to Immunity. Greber UF, Flatt JW. Annu Rev Virol. 2019 Sep 29;6(1):177-197. doi: 10.1146/annurev-virology-092818-015550. Epub 2019 Jul 5. PMID: 31283442

3. Sending mixed signals: polyomavirus entry and trafficking. Mayberry CL, Bond AC, Wilczek MP, Mehmood K, Maginnis MS. Curr Opin Virol. 2021 Apr;47:95-105. doi: 10.1016/j.coviro.2021.02.004. Epub 2021 Mar 6. PMID: 33690104

4. Parvoviral host range and cell entry mechanisms. Cotmore SF, Tattersall P. Adv Virus Res. 2007;70:183-232. doi: 10.1016/S0065-3527(07)70005-2. PMID: 17765706

Školitel

doc. Mgr. Pavel Plevka, Ph.D.

Endosome rupture is a critical yet underexplored aspect of cellular biology, with significant implications for
understanding immune responses, infection mechanisms, and drug delivery. The controlled rupture of
endosomes can lead to cargo release into the cytoplasm. Despite its importance, the precise molecular
mechanisms governing endosome rupture remain poorly understood. The student will use cryo-electron
microscopy and molecular biology tools to characterize the putative role of endosome disruption in
endocytosis of native cargo, including transferrin (clathrin-coated pit-mediated endocytosis), Anti-beta1-
adrenergic receptor (fast endophilin-mediated endocytosis), and anti-CD44/anti-CD98 (clathrin-independent
carrier / glycosylphosphatidylinositol-anchored protein-enriched early endocytic compartment mediated
endocytosis). He/she will also use cells deficient in selected mechanisms enabling endocytosis and
endosome remodeling to determine which cellular processes are responsible for endosome disruption.

Requirements on candidates:

The prospective student should be interested in learning cryo-EM and structure determination approaches.
Previous experience with molecular biology, programming, scripting, and data analyses is a plus.

More information: RG Structural Virology

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Key principles and methods for studying the endocytosis of biological and nanoparticle therapeutics. Rennick JJ, Johnston APR, Parton RG. Nat Nanotechnol. 2021 Mar;16(3):266-276. doi: 10.1038/s41565-021-00858- 8. Epub 2021 Mar 12. PMID: 33712737

2. Experimental Perspectives on Direct Visualization of Endosomal Rupture. Day RA, Sletten EM. Chembiochem. 2021 Dec 2;22(23):3277-3282. doi: 10.1002/cbic.202100379. Epub 2021 Sep 23. PMID: 34519410

3. Endosomal escape: A bottleneck for LNP-mediated therapeutics. Chatterjee S, Kon E, Sharma P, Peer D. Proc Natl Acad Sci U S A. 2024 Mar 12;121(11):e2307800120. doi: 10.1073/pnas.2307800120. Epub 2024 Mar 4. PMID: 38437552

4. Mechanisms of endocytosis. Doherty GJ, McMahon HT. Annu Rev Biochem. 2009;78:857-902. doi:10.1146/annurev.biochem.78.081307.110540. PMID: 19317650

Školitel

doc. Mgr. Pavel Plevka, Ph.D.

CDK11 is ubiquitously expressed in all tissues and the CDK11 null mouse is lethal at an early stage of development indicating an important role for Cdk11 in the adult as well as during development. CDK11 is believed to play a role in RNAPII-directed transcription and co-transcriptional mRNA-processing, particularly alternative splicing and 3end processing. However, its genome-wide function in regulating the human transcriptome is unknown. Notably, several recent studies identified CDK11 as a candidate essential gene for growth of several cancers therefore, understanding the molecular mechanism(s) of CDK11-dependent gene expression would be also of significant clinical interest. In this research we will use various techniques of molecular biology and biochemistry to characterize genome-wide role of CDK11 in regulation of gene expression and tumorigenesis.

Requirements on candidates:

Background in molecular biology, biochemistry or life sciences. Interest in bioinformatics and data analyses is desirable.

More information: RG Inherited Diseases - Transcriptional Regulation

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Hluchy M, Gajduskova, P., Ruiz de los Mozos I., Rajecky M., Kluge M., Berger BT., Slaba Z. Potesil D., Weis E., Ule J., Zdrahal Z., Knapp S., Paruch K., Friedel CC., Blazek D*. CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1. Nature; 609(7928):829-834 (2022)

2. Gajduskova, P., Ruiz de Los Mozos I, Rajecky M., Hluchy M., Ule J., Blazek D*: CDK11 is required for transcription of replication dependent histone genes. Nature Structural & Molecular Biology 27 (5):500-510 (2020)

Školitel

Mgr. Dalibor Blažek, Ph.D.

Cdk12 is transcriptional cyclin-dependent kinase (Cdk) found mutated in various cancers. In previous studies we found that Cdk12 maintains genome stability via optimal transcription of key homologous recombination repair pathway genes including BRCA1. Apart from the C-terminal domain of RNA Polymerase II other cellular substrates for both kinases are not known. In this research we propose using a screen in cells carrying an analog sensitive mutant of CDK12 to discover its novel cellular substrates. The substrates and their roles in normal and cancerous cells will be characterized by various techniques of molecular biology and biochemistry.

Requirements on candidates:

Background in molecular biology, biochemistry or life sciences. Interest in bioinformatics and data analyses is desirable.

More information: RG Inherited Diseases - Transcriptional Regulation

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

Pilarova K, Herudek J, Blazek D.*: CDK12: Cellular functions and therapeutic potential of versatile player in cancer: Nucleic Acids Research Cancer (Oxford University Press) k2 (1): zcaa003 (2020).

Chirackal Manavalan A.P., Pilarova K., Kluge M., Bartholomeeusen K., Oppelt J., Khirsariya P., Paruch K., Krejci L., Friedel C.C., Blazek D* : CDK12 controls G1/S progression via regulating RNAPII processivity at core DNA replication genes. EMBO reports 20(9):47592 (2019).

Ekumi KM, Paculova H, Lenasi T, Pospichalova V, Bösken CA, Rybarikova J, Bryja V, Geyer M, Blazek D*, Barboric M*. Ovarian carcinoma CDK12 mutations misregulate expression of DNA repair genes via deficient formation and function of the Cdk12/CycK complex. Nucleic Acids Research 43(5):2575-89 (2015).

Bösken CA, Farnung L, Hintermair C, Merzel Schachter M, Vogel-Bachmayr K, Blazek D, Anand K, Fisher RP, Eick D, Geyer M. The structure and substrate specificity of human Cdk12/Cyclin K. Nature Communications 5 (2014).

Blazek D*., Kohoutek J., Bartholomeeusen K., Johansen E., Hulinkova P., Luo Z., Cimermancic P.,Ule J., Peterlin B.M.: The CycK/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes. Genes and Development 25 (20): 2158-2172 (2011).

Školitel

Mgr. Dalibor Blažek, Ph.D.

Chronic lymphocytic leukemia (CLL) cells and indolent lymphomas are known to be dependent on diverse microenvironmental stimuli providing them signals for survival, development, proliferation, and therapy resistance. It is known that CLL cells undergo apoptosis after cultivation in vitro, and therefore it is necessary to use models of CLL microenvironment to culture CLL cells long-term and/or to study their proliferation. Several in vitro and in vivo models meet some of the characteristics of the natural microenvironment based on coculture of malignant cells with T-lymphocytes or stromal cell lines as supportive cell, but they also have specific limitations.
The aim of this research is to develop and use models mimicking lymphoid microenvironment to study novel therapeutic options, e.g. drugs targeting CLL proliferation, development of resistance in long-term culture or combinatory approaches, which cannot be analysed in experiments based on conventional culture of CLL/lymphoma primary cells. This project will utilize models developed in the laboratory and will further optimize and modify them. We have recently developed a co-culture model that is allowing to induce robust proliferation of primary CLL cells, something that was virtually impossible for decades (Hoferkova et al, Leukemia, 2024). Using kinase inhibitors, the biology of CLL and responses to targeted treatment will be interrogated. The student will utilize various functional assays, RNA sequencing, genome editing, drug screening etc., with the use of primary patient’s samples and cell lines. The research might bring new insights into the microenvironmental dependencies and development of resistance to targeted therapy.

Requirements on candidates:

Motivated smart people who have the “drive” to work independently but are also willing to learn from other people in the lab and collaborate.
Candidates should have a master’s degree in Molecular biology, Biochemistry, or a similar field and have a deep interest in molecular biology and cancer cell biology.

More information: RG Microenvironment of Immune Cells

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Hoferkova E, et al…. Mraz M. Stromal cells engineered to express T cell factors induce robust CLL cell proliferation in vitro and in PDX co-transplantations allowing the identification of RAF inhibitors as anti-proliferative drugs. Leukemia. 2024 Aug;38(8):1699-1711

2. Pavlasova G, et al…. Mraz M. Ibrutinib inhibits CD20 upregulation on CLL B cells mediated by the CXCR4/SDF-1 axis. Blood. 2016 Sep 22;128(12):1609-13. doi: 10.1182/blood-2016-04-709519. Epub 2016 Aug 1. PMID: 27480113 Free PMC article

3. Kipps et al. Chronic lymphocytic leukaemia. Nat Rev 2017 https://pubmed.ncbi.nlm.nih.gov/28102226/

4. Seda V, Mraz M. B-cell receptor signalling and its crosstalk with other pathways in normal and malignant cells. Eur J Haematol. 2015 Mar;94(3):193-205. doi: 10.1111/ejh.12427. Epub 2014 Sep 13. PMID: 25080849 Review.

Školitel

prof. MUDr. Mgr. Marek Mráz, Ph.D.

Posttranscriptional RNA modifications possess key roles in diverse pathways in
humans, including development, disease and infections. This PhD project will focus on
the machines and role of internal RNA modifications of coding and noncoding RNAs in
human cells. The student will master diverse methodologies, such as human cell
culture manipulations (cultivation, RNAi, CRISPR/Cas9, etc.), recombinant DNA
preparation, protein expression and purification, high-throughput analyses and
enzymatic assays. She/he will have the opportunity to present the results at
prestigious international conferences. Moreover, this project will involve collaboration
with other leading researches in European institutes.

Requirements on candidates:

Prospective students should ideally have a master's degree in molecular biology/biochemistry and have laboratory experience in nucleic acids and/or protein purification and analyses. Experience with coding in R and statistics is a big plus. The most highly valued feature, however, is excitement and curiosity for science and a strong drive in tackling important biological questions.

More information: RG RNA Quality Control

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Školitel

prof. Mgr. Štěpánka Vaňáčová, Ph.D.

Dynamic transitions between B-DNA and non-canonical DNA conformations, such as G-quadruplexes, i-motifs, and Z-DNA, contribute to the regulatory control of genome integrity and gene expression, playing an essential role in defense against invading pathogens. The function of these structures is linked to their dynamic polymorphism, which allows them to adapt sensitively to changes in the intracellular environment due to cellular stress and physiological oscillations. The project will explore the mechanisms of transferring information from the intracellular environment to the dynamic structural equilibria of DNA as the cell’s physiological state changes.

Requirements on candidates:

The candidate is expected to have theoretical and practical knowledge of biomolecular NMR spectroscopy and an interest in the biology of nucleic acids.

More information: RG Non-Coding Genome

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link)

Poznámky

Recommended literature:

1: Víšková et al. In-cell NMR suggests that DNA i-motif levels are strongly depleted in living human cells. Nat Commun. 2024 Mar 5;15(1):1992.

2: Krafcikova et al. Monitoring DNA-Ligand Interactions in Living Human Cells Using NMR Spectroscopy. J Am Chem Soc. 2019 Aug 28;141(34):13281-13285.

3: Gajarsky et al. DNA Quadruplex Structure with a Unique Cation Dependency. Angew Chem Int Ed Engl. 2024 Feb 12;63(7):e202313226.

Školitel

doc. Mgr. Lukáš Trantírek, Ph.D.

Cells form dynamic clusters of liquid protein droplets that act as nanoreactors or storage sites,
increasing the local concentration of specific protein components. These membrane-less
organelles self-assemble based on weak protein-protein interactions between intrinsically
disordered domains. Although specific cellular conditions can alter these interactions, the
relationship between the two remains unclear. This project focuses on the droplets involved in
genome transcription, where post-translational modifications control droplet composition and
regulate transcription. The project will explore the relationship between sequence and
environment using multi-scale simulations, advanced sampling techniques, and novel protein
parameterizations. The research is closely linked to collaborations with leading experimental
teams and will be discussed in more detail during the interview. The expected findings are
important not only for the fundamental understanding of biological processes but could also aid
in designing new treatments for numerous diseases, including cancer.

Requirements on candidates:

Outstanding candidates with experience in computer simulations and with an MSc/PhD degree in
the fields of biophysics, soft matter physics, physical chemistry, computational chemistry,
statistical mechanics, or related fields. Experience with molecular dynamics simulations (with
GROMACS, CHARMM, NAMD, AMBER, LAMMPS, etc.) at the atomistic or coarse-grained level
would be an advantage.

More information: RG Interaction Protein-Protein and Protein-Membrane

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Biochemistry 2022, 61, 2456-2460 , doi: 10.1021/acs.biochem.2c00220

2. Nucleus 2023, 14:1, 2213551, doi: 10.1080/19491034.2023.2213551

3. PLoS Comput Biol 2023, 19(7): e1011321. doi: 10.1371/journal.pcbi.1011321

4. Science 2018, 361, 6, 6400, doi: 10.1126/science.aar2555

Školitel

prof. RNDr. Robert Vácha, PhD.

The project goal is to understand the molecular machinery that regulates the migration of malignant B cells between different niches such as lymphoid and bone marrow niche and peripheral blood. This is of great interests a general mechanism of how migration is regulated in cancer cells, but also especially in chronic lymphocytic leukemia (CLL), which is a disease dependent on the B cell recirculation between different compartments (reviewed in Seda and Mraz, 2015; Seda et al, 2021). In CLL, but also in other lymphomas, the malignant B cells permanently re-circulate from peripheral blood to lymph nodes and back, and blocking this recirculation can be used therapeutically since malignant B cells depend on signals in the immune microenvironment. However, the factors that regulate this are mostly unclear. The lab established several models for in vitro and in vivo studies of microenvironmental interactions and their interplay (Hoferkova et al, Leukemia, 2024; Pavlasova et al. Blood, 2016; Pavlasova et al. Leukemia, 2018; Musilova et al. Blood, 2018; Mraz et al. Blood, 2014; Cerna et al. Leukemia, 2019).
We have identified candidate molecules that might act as novel regulators of the B cell migration or the balance between homing and survival in peripheral blood. This will be further investigated by the PhD student using technics such as genome editing (CRISPR), RNA sequencing, use of primary samples, functional studies with various in vitro and in vivo mouse models. The research is also relevant for understanding resistance mechanisms to BCR inhibitors, pre-clinical development of novel drugs and their combinations (several patents submitted by the lab).

Requirements on candidates:

Motivated smart people who have the “drive” to work independently but are also willing to learn from other people in the lab and collaborate.
Candidates should have a master’s degree in Molecular biology, Biochemistry, or a similar field and have a deep interest in molecular biology and cancer cell biology.

More information: RG Microenvironment of Immune Cells

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Seda et al….Mraz FoxO1-GAB1 Axis Regulates Homing Capacity and Tonic AKT Activity in Chronic Lymphocytic Leukemia. Blood 2021 March (epub). https://pubmed.ncbi.nlm.nih.gov/33786575/

2. Pavlasova G, et al…. Mraz M. Ibrutinib inhibits CD20 upregulation on CLL B cells mediated by the CXCR4/SDF-1 axis. Blood. 2016 Sep 22;128(12):1609-13. doi: 10.1182/blood-2016-04-709519. Epub 2016 Aug 1. PMID: 27480113 Free PMC article

3. Seda V, Mraz M. B-cell receptor signalling and its crosstalk with other pathways in normal and malignant cells. Eur J Haematol. 2015 Mar;94(3):193-205. doi: 10.1111/ejh.12427. Epub 2014 Sep 13. PMID: 25080849 Review.

Školitel

prof. MUDr. Mgr. Marek Mráz, Ph.D.

In response to stress, protein synthesis comes to a halt and cells assemble specific
biomolecular condensates known as stress granules (SGs), remodelling the cellular
program towards a specialized active response to counteract the stress. This project
aims to dissect this response in plants.
The student will investigate the stress-specialized translation initiation complex eIF4F
and determine its biological role under SGs formation. It is expected that the student will
become an expert in cellular biology, utilizing advanced microscopy techniques (confocal
and super-resolution microscopy) and common molecular biology techniques, to
visualize from protein complexes to single RNA molecules.

Requirements on candidates:

We are looking for a highly motivated PhD student with an interest in cellular biology and
advanced microscopy techniques. Ideally the candidate should have acquired basic
expertise in plant molecular biology techniques. Confocal microscopy is a plus although
it is not required.

More information: RG Plant Molecular Biology

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Banani, S. F., Lee, H. O., Hyman, A. A. & Rosen, M. K. Biomolecular condensates:Organizers of cellular biochemistry. Nature Reviews Molecular Cell Biology vol. 18 (2017).

2. Cairo, A. et al. Meiosis exit in Arabidopsis is driven by P-body-mediated inhibition of translation. Science (80-. ). 377, (2022).

3. Cho, H. Y., Lu, M. Y. J. & Shih, M. C. The SnRK1-eIFiso4G1 signaling relay regulates the translation of specific mRNAs in Arabidopsis under submergence. New Phytol. 222, (2019).

4. Chantarachot, T. & Bailey-Serres, J. Polysomes, stress granules, and processing bodies: A dynamic triumvirate controlling cytoplasmic mRNA fate and function. Plant Physiology vol. 176 (2018).

5. Desroches Altamirano, C. et al. eIF4F is a thermo-sensing regulatory node in the translational heat shock response. Mol. Cell (2024) doi:10.1016/J.MOLCEL.2024.02.038.

Školitel

Mgr. Karel Říha, Ph.D.

Ribosome assembly is a complex, multi-stage process essential for cellular function. It involves the
coordinated folding, modification, and binding of ribosomal RNAs (rRNAs) and proteins (r-proteins) with the
assistance of various assembly factors. The absence or dysfunction of these factors often results in slow
cell growth and improper ribosome assembly. Under such stress conditions, cells may employ stress-related
factors to regulate ribosome assembly. However, the biological and structural connections between
ribosome assembly and the stress response remain poorly understood compared to other aspects of
ribosome function.
This thesis aims to unravel the intricate relationship between ribosome biogenesis and stress response
mechanisms in bacteria and archaea. By analysing ribosomal fractions from bacterial strains lacking key
maturation factors, we seek to identify novel ribosome-associated factors or repurposed translation factors
involved in ribosome reassembly. Single-particle cryo-electron microscopy will provide structural insights
into ribosome reassembly processes using ex vivo ribosomal complexes. Additionally, the investigation of
the archaeal translation system, an understudied area, may reveal novel proteins linked to ribosome
maturation. This research promises to uncover previously unknown mechanisms of ribosome reassembly in
bacteria with defective ribosome maturation and identify novel factors influencing ribosome assembly in
archaea.

Requirements on candidates:

We are seeking a PhD. candidate who was trained in structural biology (mainly cryo-electron microscopy),
worked in translation field or in general biochemistry and is a motivated person with collaborative mind set.

More information: RG Regulation of Translation

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Klinge, S. and J. L. Woolford, Jr. (2019). Ribosome assembly coming into focus. Nat Rev Mol Cell Biol 20(2): 116-131.

2. Khusainov, I., et al. (2020). Mechanism of ribosome shutdown by RsfS in Staphylococcus aureus revealed by integrative structural biology approach. Nat Commun 11(1): 1656.

3. Sharma, I. M. and S. A. Woodson (2020). RbfA and IF3 couple ribosome biogenesis and translation initiation to increase stress tolerance. Nucleic Acids Res 48(1): 359-372.

4. Nikolay, R., et al. (2021). Snapshots of native pre-50S ribosomes reveal a biogenesis factor network and evolutionary specialization. Mol Cell 81(6): 1200-1215 e1209.

5. Yaeshima, C., et al. (2022). A novel ribosome-dimerization protein found in the hyperthermophilic archaeon Pyrococcus furiosus using ribosome-associated proteomics. Biochem Biophys Res Commun 593: 116-121.

Školitel

Mgr. Gabriel Demo, Ph.D.

The main neuropathological signs of Alzheimer’s disease are associated with the
fibrillization of tau protein into neurofibrillary tangles. The growing number of Tau fibrils
allow the structural and stability elucidations Studying how different factors influence
the formation of protein fibrils is the key to understanding these neurodegenerative
processes. The main aim of this PhD project will be computational simulations of
structural changes leading to the fibril form of selected proteins (Tau, a-Syn, Abeta) and
the corresponding free energy profiles along such pathways. The impact of
phosphorylation, buffer conditions, truncation, or the interaction with the client
proteins like 14-3-3s will be addressed. The obtained computational data will be
validated by biophysical experimental techniques.

Requirements on candidates:

Preferable candidate’s background in biophysics, computational chemistry, or physical
chemistry.

More information: RG Protein Structure and Dynamics

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Kitoka K, Lends A, Kučinskas G, Bula AL, Krasauskas L, Smirnovas V, Zilkova M; Kovacech B, Skrabana R, Hritz J, Jaudzems K*: dGAE(297-391) tau fragment promotes the formation of CTE-like full-length tau filaments, Angew. Chem. Int. Ed. 2024, e202407821.

2. Crha R., Kozeleková A., Hofrová A., Iľkovičová L., Gašparik N., Kadeřávek P., Hritz J.*: Hiding in plain sight: Complex interaction patterns between Tau and 14-3-3 zeta protein variants. . Int. J. Biol. Macromol. 2024, 266, 130802.

3. Lasorsa A., Bera K., Malki I., Dupré E., Cantrelle F., Merzougui H., Sinnaeve D., Hanoulle X., Hritz J.*, Landrieu I.*: Conformational impact of multiple phosphorylations within BIN1 SH3 domain binding site in the proline rich region of Tau protein. Biochemistry 2023, 62, 1631–1642.

4. Trosanova Z., Lousa P., Kozelekova A., Brom T., Gasparik N., Tungli J., Weisova V., Zupa E., Zoldak G., Hritz J.*: Quantitation of human 14-3-3 zeta dimerization and the effect of phosphorylation on dimer-monomer ekvilibria. J. Mol. Biol. 2022, 434, 167479.

5. Zapletal, V.; Mládek, A.; Melková, K.; Louša, P.; Nomilner, E.; Jaseňáková, Z.; Kubáň, V.; Makovická, M.; Laníková, A.; Žídek L.; Hritz, J.* Choice of force field for proteins containing structured and intrinsically disordered regions. Biophys. J. 2020, 118, 1621 – 1633.

6. Jandova Z; Trosanova Z.; Weisova V.; Oostenbrink C., Hritz J.*: Free energy calculations on the stability of the 14-3-3 zeta protein. BBA - Proteins and Proteomics, 2018, 1866, 442- 450.

7. Nagy G., Oostenbrink C., Hritz J.*: Exploring the Binding Pathways of the 14-3-3 zeta Protein: Structural and Free-Energy Profiles Revealed by Hamiltonian Replica Exchange Molecular Dynamics with Distance Field Distance Restraints. PLoS ONE 2017,12(7), e0180633.

Školitel

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

Despite decades of study, important aspects of phage replication cycles, such as the mechanism of genome
delivery, initiation of head assembly, and genome packaging, are poorly understood. We propose to use
cryo-electron microscopy and tomography to characterize replication intermediates of phage LE3 infecting
Leptospira. The in situ data collection will be enabled by the dimensions of leptospira cells, which are 100 nm
thin. Analysis of the infection intermediates will focus on genome delivery, initiation of head assembly, and
genome packaging. These processes cannot be studied in vitro because of the challenges of preparing the
corresponding complexes in functional form in sufficient amounts.

Requirements on candidates:

The prospective student should be interested in learning cryo-EM and structure determination approaches.
Previous experience with molecular biology, programming, scripting, and data analyses is a plus.

More information: RG Structural Virology

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link)

Poznámky

Recommended literature:

1. Characterization of LE3 and LE4, the only lytic phages known to infect the spirochete Leptospira. Schiettekatte O, Vincent AT, Malosse C, Lechat P, Chamot-Rooke J, Veyrier FJ, Picardeau M, Bourhy P. Sci Rep. 2018 Aug 6;8(1):11781. doi: 10.1038/s41598-018-29983-6.

2. Molecular architecture of tailed double-stranded DNA phages. Fokine A, Rossmann MG. Bacteriophage. 2014 Jan 1;4(1):e28281. doi: 10.4161/bact.28281. Epub 2014 Feb 21. PMID: 24616838

3. A century of the phage: past, present and future. Salmond GP, Fineran PC. Nat Rev Microbiol. 2015 Dec;13(12):777-86. doi: 10.1038/nrmicro3564. Epub 2015 Nov 9. PMID: 26548913

4. Viral genome packaging machines: Structure and enzymology. Catalano CE, Morais MC. Enzymes. 2021;50:369-413. doi: 10.1016/bs.enz.2021.09.006. Epub 2021 Nov 10. PMID: 34861943

5. Casjens, S. R. (2011). The DNA-packaging nanomotor of tailed bacteriophages. Nature Reviews Microbiology, 9(9), 647–657. doi:10.1038/nrmicro2632

Školitel

doc. Mgr. Pavel Plevka, Ph.D.

The PhD project is a continuation of previous studies of the research group, in collaboration with the Libor
Krasny of Institute of Microbiology, Academy of Sciences of The Czech Academy of Sciences. Krasny’s lab
discovered several proteins of Gram-positive bacteria that play so far little understood roles in transcription
regulation. The goal of the project is to combine structural biology approaches to establish relation between
structure, biophysical properties, and function of these proteins and other poorly understood bacterial
transcription factors. The particular aims include maping of transient interactions of the delta subunit with
the RNA polymerase core of Bacillus subtilis, interplay between delta subunit and sigma factors, interactions
of a recently discovered transcription factor MoaB2 with mycobacterial sigma factors and RNA polymerases.
Cryo-electron microscopy will be used as a major tool to study structures of the proteins in complexes with
RNA polymerase. A particular attention will be paid to dynamics of the proteins, that often contain large
disordered regions, where cryo-EM data will be combined with results of NMR spectroscopy. As alternative
methods, FRET (and potentially EPR in collaboration with V. Laguta) using advanced labelling techniques
will be used. The project should result in publications in respected journals with the student being the
(shared) first author.

Requirements on candidates:

Strong background in biophysics and/or physical chemistry, experience with electron microscopy or NMR
spectroscopy is an advantage.

More information: RG Protein Structure and Dynamics

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

Poznámky

Recommended literature:

1. Camacho-Zarco et al., Chem. Reviews. 2022, 122, 9331-9356 https://dx.doi.org/10.1021/acs.chemrev.1c01023.

2. Kubáň et al., J. Am. Chem. Soc. 2019, 141, 16817-16828. https://dx.doi.org/10.1021/jacs.9b07837.

Školitel

prof. Mgr. Lukáš Žídek, Ph.D.

The project is focused on detailed structural characterization of short purine oligonucleotides clipped by proper sequential motifs that induce parallel orientation of DNA strands. For this purpose, NMR experiments combined with MD simulations will be employed. The effect of modifications of selected nucleotides on the structural properties of designed models will be investigated to gain deeper understanding of key interactions that contribute to the folding of such systems.

Requirements on candidates:

Computational and quantum chemistry, structural chemistry or biology.

More information: RG Structure of Biosystems and Molecular Materials

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).

 

Poznámky

Recommended literature:

Aleš NOVOTNÝ, Jan NOVOTNÝ, Iva KEJNOVSKÁ, Michaela VORLÍČKOVÁ, Radovan FIALA and Radek MAREK. Revealing structural peculiarities of homopurine GA repetition stuck by i-motif clip. Nucleic Acids Research, 2021, 49, 11425. doi:10.1093/nar/gkab915

Školitel

prof. RNDr. Radek Marek, Ph.D.

Proteins are produced by ribosome-catalyzed translation of mRNAs in all domains of life. Translation is also critical in the context of human host-pathogen interaction where the ribosome, as the central molecular machine for genetic information expression, is the subject to numerous regulatory and quality control events and pathological interventions. The strategies adopted by viruses to reprogram translation and co-translational quality control machinery to promote infection are poorly understood. Thus, there is an urgent need for further research in this area to develop effective strategies for combating viral infections. The successful candidate will study how viruses affect human translation and co-translational quality control with the aim of providing high-resolution structures of large macromolecular assemblies. He/she will utilize human cell cultures, protein expression and purification techniques and biochemistry methods to produce samples for cryogenic electron microscopy (cryo-EM). Comprehensive training in cryo-EM will be available to the successful candidate.

Requirements on candidates:

The ideal candidate should have a background in either molecular biology, biochemistry, or structural biology. Experience with human cell culture work or protein biochemistry is a plus.

More information: RG Translation Control

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link)

 

Poznámky

Recommended literature:

Xu, Z., et al., SARS-CoV-2 impairs interferon production via NSP2-induced repression of mRNA translation. Proc Natl Acad Sci U S A, 2022. 119(32): p. e2204539119.

Hsu, J.C., et al., Viperin triggers ribosome collision-dependent translation inhibition to restrict viral replication. Mol Cell, 2022. 82(9): p. 1631-1642 e6.

Thoms, M., et al., Structural basis for translational shutdown and immune evasion by the Nsp1 protein of SARS-CoV-2. Science, 2020. 369(6508): p. 1249-1255.

Lu, B., Translational regulation by ribosome-associated quality control in neurodegenerative disease, cancer, and viral infection. Front Cell Dev Biol, 2022. 10: p. 970654.

Školitel

RNDr. Petr Těšina, Ph.D.