Vědy o živé přírodě

1. Wang X. et al. Structure of Rift Valley Fever Virus RNA-Dependent RNA Polymerase. Journal of Virology (2022).
2. Arragain B. et al. Pre-initiation and elongation structures of full-length La Crosse virus polymerase reveal functionally important conformational changes. Nature Communications (2020).
3. Arragain B. et al. Structural snapshots of La Crosse virus polymerase reveal novel insights into replication and transcription mechanisms. Nature Communications (2022).

• Experience in molecular biology, biochemistry, or virology.
• Practical laboratory experience with protein purification, human cell cultures, or RNA biology.
• Basic knowledge of structural biology techniques, particularly cryo-electron microscopy.
• Interest in host-pathogen interactions and viral gene expression.
• Ability to work independently and collaboratively in an interdisciplinary environment.
• Good written and spoken English.

Školitel

Mgr. Gabriel Demo, Ph.D.

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.

Školitel

doc. Mgr. Pavel Plevka, Ph.D.

Školitel

Mgr. Dalibor Blažek, Ph.D.

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

Školitel

prof. MUDr. Mgr. Marek Mráz, Ph.D.

Recommended literature:
1. Filbeck, S., et al., Ribosome-associated quality-control mechanisms from bacteria to humans. Mol Cell, 2022. 82(8): p. 1451-1466.
2. Ikeuchi, K., et al., Collided ribosomes form a unique structural interface to induce Hel2-driven quality control pathways. EMBO J, 2019. 38(5).
3. Saito, K., et al., Ribosome collisions induce mRNA cleavage and ribosome rescue in bacteria. Nature, 2022. 603(7901): p. 503-508.
4. Narita, M., et al., A distinct mammalian disome collision interface harbors K63-linked polyubiquitination of uS10 to trigger hRQT-mediated subunit dissociation. Nat Commun, 2022. 13(1): p. 6411.
5. Wu, C.C., et al., Ribosome Collisions Trigger General Stress Responses to Regulate Cell Fate. Cell, 2020. 182(2): p. 404-416 e14.
 

Školitel

RNDr. Petr Těšina, Ph.D.

Školitel

doc. Mgr. Pavel Plevka, Ph.D.

Školitel

Mgr. Dalibor Blažek, Ph.D.

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website
Annotation: 
Paramyxoviruses are membrane-enveloped RNA viruses that include major human pathogens such as measles and mumps viruses, as well as highly lethal emerging zoonotic viruses such as Nipah virus, which causes encephalitis with case fatality rates exceeding 50%. Despite their medical importance, there are currently no specific antiviral therapies targeting paramyxovirus infection.
A promising antiviral target is the process of virus assembly and budding, which is orchestrated by the viral matrix protein. Matrix acts as a molecular scaffold at the host-cell plasma membrane, coordinating the recruitment of viral components and driving membrane remodelling to enable virus release. However, current models do not fully explain how matrix specifically recognises the plasma membrane, selectively engages other viral components, and coordinates the timing of budding from the host cell.
This PhD project will investigate the structure and assembly mechanisms of selected paramyxoviruses both in situ and in vitro, using state-of-the-art cryo-electron microscopy approaches. Single-particle cryo-EM analysis will be used to determine the architecture of purified virions and to define the spatial relationships between individual viral components. Focused ion beam milling, cryo-electron tomography and subtomogram averaging will then be applied to visualise viral assembly and budding directly within virus-producing cells.
These in situ studies will be complemented by in vitro reconstitution of viral components on synthetic lipid membranes. These minimal systems will enable high-resolution cryo-EM analysis of matrix-membrane assemblies and dynamic fluorescence-based studies of assembly behaviour. Together, the project will provide new mechanistic insight into how paramyxoviruses assemble and bud from host cells.
Requirements for candidate:
Applicants should have a strong background in one or more of the following areas or related fields: structural biology, molecular biology, biochemistry, virology or biophysics. Experience with Linux-based systems and scripting would be advantageous, but is not essential.
We are equally interested in candidates who are enthusiastic about science, motivated by the project topic, keen to learn new experimental and computational methods, and driven to tackle important and challenging scientific questions. Hard skills are valuable, but curiosity, commitment and scientific ambition will be valued just as highly.

Recommended literature:
Watkinson RE, Lee B. Nipah virus matrix protein: expert hacker of cellular machines. FEBS Lett. 2016;590(15):2494-2511. doi:10.1002/1873-3468.12272

Norris MJ, Husby ML, Kiosses WB, et al. Measles and Nipah virus assembly: Specific lipid binding drives matrix polymerization. Sci Adv. 2022;8(29):eabn1440. doi:10.1126/sciadv.abn1440

Clemente CM, Mobarec JC, Bharat TAM. Applications and prospects of cryo-electron tomography in drug discovery and understanding disease. Curr Opin Struct Biol. 2026;98:103283. doi:10.1016/j.sbi.2026.103283

Školitel

Mgr. Dominik Hrebík, Ph.D.

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

Školitel

prof. MUDr. Mgr. Marek Mráz, Ph.D.

Školitel

doc. Mgr. Pavel Plevka, Ph.D.

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website
Annotation: 
The bottom-up construction of an autonomously dividing minimal cell would represent a major advance in synthetic cell biology and provide a stringent test of our understanding of the fundamental principles of life, particularly the mechanisms that drive cell division. Decades of research have established Bacillus subtilis as a model organism for studying cell division in Gram-positive bacteria. However, despite substantial progress, a high-resolution structure of the bacterial division machinery remains elusive.
This PhD project will investigate the structure and assembly mechanism of the bacterial division Z-ring both in situ and in vitro, using a combination of focused ion beam milling, cryo-electron tomography, subtomogram averaging and single-particle cryo-EM analysis. The student will first optimise strategies to arrest cell division at a defined stage, enabling Z-ring structures to be averaged across multiple cells. They will then develop an approach for orienting cells perpendicular to the cryo-EM grid, facilitating downstream FIB-milling and high-resolution cryo-electron tomography.These methods will be used to determine the architecture of the Z-ring in its native cellular context.
In parallel, the student will support the in situ observations with in vitro reconstitutions of the division complex on artificial membranes, followed by structural analysis using cryo-EM. Together, these approaches will provide new insight into the molecular organisation and assembly of the bacterial cell division machinery, with broader implications for the design of antibiotics targeting cell division, synthetic cell biology and the design of minimal dividing cells.
Requirements for candidate:
Applicants should have a strong background in one or more of the following areas or related fields: structural biology, molecular biology, biochemistry or biophysics. Experience with Linux-based systems and scripting would be advantageous, but is not essential.
We are equally interested in candidates who are enthusiastic about science, motivated by the project topic, keen to learn new experimental and computational methods, and driven to tackle important and challenging scientific questions. Hard skills are valuable, but curiosity, commitment and scientific ambition will be valued just as highly.
Recommended literature:
Cameron TA, Margolin W. Insights into the assembly and regulation of the bacterial divisome. Nat Rev Microbiol. 2024;22(1):33-45. doi:10.1038/s41579-023-00942-x

Clemente CM, Mobarec JC, Bharat TAM. Applications and prospects of cryo-electron tomography in drug discovery and understanding disease. Curr Opin Struct Biol. 2026;98:103283. doi:10.1016/j.sbi.2026.103283

Errington J, Wu LJ. Cell Cycle Machinery in Bacillus subtilis. Subcell Biochem. 2017;84:67-101. doi: 10.1007/978-3-319-53047-5_3. PMID: 28500523; PMCID: PMC6126333.

Klumpe S, Plitzko JM. Cryo-focused ion beam milling for cryo-electron tomography: Shaping the future of in situ structural biology. Curr Opin Struct Biol. 2025;94:103138. doi:10.1016/j.sbi.2025.103138

Školitel

Mgr. Dominik Hrebík, Ph.D.

Školitel

doc. Mgr. Pavel Plevka, Ph.D.

Annotation: 
Every organism faces a constant battle against invading genetic elements such as viruses and plasmids. To survive, bacteria and archaea have evolved a remarkable diversity of immune systems that detect and eliminate foreign DNA. Traditionally, these systems have been studied as independent defense mechanisms. However, recent discoveries suggest that some immune systems cooperate, forming more complex defense networks capable of responding to a broader range of threats.

One particularly intriguing example is provided by prokaryotic Argonaute proteins (pAgos), programmable nucleic-acid recognition factors found throughout bacteria and archaea. While some pAgos directly destroy invading DNA, many are genetically associated with proteins belonging to entirely different immune pathways. Why these systems became linked during evolution and how they cooperate at the molecular level remains unknown.
This PhD project will investigate how Argonaute proteins interact with partner immune systems to create novel defense strategies. Using state-of-the-art electron cryomicroscopy (cryo-EM), the student will determine structures of immune complexes captured at different stages of substrate recognition, remodeling, and processing. These structural studies will be complemented by biochemical, biophysical, microbiological, and evolutionary analyses performed in collaboration with leading international laboratories.
A particular focus will be understanding how catalytically inactive Argonautes have evolved into programmable regulators of partner immune proteins and how such cooperation increases the complexity and robustness of microbial immunity. By visualizing molecular machines in action and uncovering their dynamic mechanisms, the student will reveal fundamental principles governing the evolution and organization of immune systems.
The project sits at the interface of structural biology, microbiology, evolutionary biology, and biophysics, providing training in cryo-EM, protein biochemistry, computational structural biology, and molecular mechanism discovery.
Join us to uncover how evolution creates new immune systems by combining existing ones into more powerful defense machines.

Requirements for candidate:
Biochemistry/molecular biology/strucktural biology
Recommended literature:
1) Koopal B. et al. Diverse prokaryotic Argonaute-associated immune systems. Science (2023).
2) Ugarte R. et al. Molecular mechanisms of Argonaute-associated defense systems. Mol Cell (2025).
3) Makarova KS et al. Evolutionary classification of CRISPR-Cas systems. Nat Rev Microbiol (2020).
4) Swarts DC et al. Prokaryotic Argonautes: mechanisms and biological roles. Nat Rev Microbiol.
5) Finocchio G. et al. Cooperation between prokaryotic immune systems.
 

Školitel

prof. Mgr. Richard Štefl, Ph.D.