DNA forms not only the canonical duplex but also various non-canonical structures such as triplex, G-quadruplex, and i-motif. The are many external factors that influence folding and stability of the individual forms. Further, DNA structure can be affected by attachment of various artificial covalent or noncovalent ligands.

Our investigations are focused on detailed structural characterization of short purine oligonucleotides clipped by proper sequential blocks. For this purpose, modern NMR experiments combined with MD simulations are employed. The effect of modification of selected nucleotide on the structural properties of designed models is characterized to gain deeper understanding of key noncovalent interactions that contribute to the DNA folding.

Examples of PhD topics:
a) Structure of parallel forms of nucleic acids studied by NMR spectroscopy and molecular modelling
b) Designing modified DNA fragments

More information:
radek.marek@ceitec.muni.cz
jan.novotny@ceitec.muni.cz

Notes

Note: All candidates should contact R. Marek for informal discussion before initiating the formal application process.

Supervisor

prof. RNDr. Radek Marek, Ph.D.

V současné době máme k dispozici nadkritické množství informací ohledně proteinových strukturních rodin. Konkrétně, pro většinu rodin známe stovky struktur jejích zástupců, přičemž tyto struktury pocházejí z různých organismů, některé z nich váží rozličné ligandy a mnohé obsahují různorodé mutace. Tyto informace umožňují analýzu „anatomie“ daných proteinových rodin. Například studium elementů sekundární struktury (šroubovic a skládaných listů), jejich vzájemného uspořádání, konzervovanosti a určování, které z těchto elementů jsou pro danou proteinovou rodinu klíčové a které se vyskytují jen raritně. Dále pak zkoumání proteinových tunelů a pórů, jejich charakteristik a četnosti jejich výskytu u jednotlivých zástupců proteinové rodiny. V rámci laboratoře LCC jsou vyvíjeny softwarové nástroje pro realizaci výše uvedených analýz, např. software MOLE, LiteMol, SecStrAnalyzer. Hlavním cílem disertační práce je zaměřit se na několik konkrétních biologicky významných proteinových rodin (např. cytochromy, poriny, dehalogenázy, proapoptotické proteiny) a provést jejich detailní analýzu. Dalším cílem je spolupráce při vývoji uvedených softwarových nástrojů.

Notes

Vypsáno pro přihlášení studentky Jany Porubské.

Supervisor

doc. RNDr. Radka Svobodová, Ph.D.

V současné době jsou v rámci pokročilých bioinformatických, biochemických a biologických experimentů produkována rozsáhlá data – např. elektronové hustoty z kryoelektronové mikroskopie, obrazová data získaná optickou mikroskopií, proteinové struktury produkované molekulovou dynamikou nebo coarse-grained simulacemi. Taková data obsahují cenné informace pro vědeckou komunitu. Jejich získání je však často velmi časově i finančně náročné. V mnoha případech se jedná o data netriviálně komplikovaná (různě strukturované souborové hierarchie a závislosti mezi nimi) a velmi rozsáhlá. Stále častějším a do budoucna povinným požadavkem vědecké komunity je zpřístupňovat data dle FAIR principů. Tzn. že je nezbytné tato data vhodně strukturovat, anotovat a archivovat, aby byla pro komunitu dostupná, transparentně vyhledatelná, uložena ve standardních formátech a tím dále opakovaně využitelná. A právě vývojem workflow pro management uvedených dat se bude zabývat tato disertační práce.

Supervisor

doc. RNDr. Radka Svobodová, Ph.D.

Bacterial and fungal infections are once again becoming a serious threat to humans. Especially with the emergence of new strains resistant to known antibacterial and antifungal drugs, the search for new treatments has become paramount. However, the classical drug development approaches have many limitations and have not provided successful candidates in the last decades. Hopefully, the situation can change due to a steady increase in computational power. Such unprecedented computational power, combined with new algorithms employing machine learning and artificial intelligence approaches, has the potential to revolutionize structural biology, biomolecular chemistry, and bioinformatics. However, many challenges need to be overcome to get the required outcome.

We are interested in combining in silico modelling approaches utilizing both physically based and machine learning approaches to understand the function of enzymes from pathogenic organisms. Detailed knowledge of protein behaviour and enzymatic reaction mechanisms is essential for developing potential inhibitors and, thus, novel drugs capable of blocking specific biochemical pathways that either kill the pathogen or help the immune system eradicate the infection.

We focus on systems with unknown experimental structures, where the combination of artificial intelligence approaches inspired by AlphaFold2 methodology and advanced molecular dynamics sampling can reveal a suitable structural model. The found model is then employed in the subsequent study of the reaction mechanisms by hybrid approaches utilizing reaction and classical potentials. We test the suitability of many approaches, from a traditional quantum mechanical description of the active site to modern ones based on machine learning approaches or reactive potentials such as ReaxFF. We employ the in-house developed PMFLib software to obtain free energies describing the reaction and activation energies of the studied processes.

Possible PhD topics include:

• Structure, protein dynamics, and reaction mechanisms of fucosyltransferases
• Pharmacologically relevant glycosyltransferases in Mycobacterium tuberculosis

Notes

Téma vyhrazeno pro studenta Július Zemaník.

Supervisor

RNDr. Petr Kulhánek, Ph.D.

Correlative Light Electron Microscopy (CLEM) uses a combination of an optical (fluorescence) microscope and a cryo-electron microscope. Two images of the sample are taken simultaneously – one with the optical light, the other with the electron beam. This technology allows to capture not only dynamic changes but also the molecular ultrastructure of living systems. New developments in accurate positional referencing of specimens on mounting grids, advances in the instrumentation, and the availability of software packages for cross-platform data correlation allow to image the ultrastructure of nucleolar sub-compartments and to track specific proteins found in phase-separated organelles. In this project, we will implement the CLEM technology to investigate and visualize phase-separated organelles involved in transcription by RNA polymerase II and investigate their regulatory mechanism during transcription. This biophysically focused project will also involve other imaging approaches, including single-particle reconstruction cryo-electron microscopy and cryo-electron tomography, which will help to obtain an overall picture of condensate-based transcription at different resolutions.

Supervisor

prof. Mgr. Richard Štefl, Ph.D.

Současné chemické, biochemické i biologické experimentálních metody produkují mnoho různorodých výstupních dat. Tato data jsou nejen důležitou součástí publikací, ale i velmi cenným materiálem k dalším analýzám. Proto v rámci grantových projektů i přímo mezi výzkumnými pracovníky silně vyvstává potřeba strukturovaného zaznamenávání výstupních dat a postupů, realizovaných v průběhu experimentů.  

K tomuto účelu začala být v posledních letech intenzivně vyvíjena softwarová řešení – takzvané elektronické laboratorní deníky (ELN). Vývoj těchto softwarových nástrojů v současné době dynamicky probíhá a je dostupno několik desítek open source i komerčních řešení. Pro výzkumné pracovníky je velkou výzvou zjistit, který z těchto nástrojů je vhodný pro jejich laboratoř a integrovat jej do datového workflow své laboratoře. A právě na tuto oblast je cílena disertační práce. 

Konkrétní úkoly práce jsou: Zorientovat se v pluralitě ELN, analyzovat současnou situaci a vyhledat vhodná řešení pro vybrané typy laboratoří. Integrovat ELN do bioinformatických datových workflow vybraných laboratoří a případně provést adaptace a rozšíření ELN, nutné pro jejich efektivní využívání.

Notes

The topic is reserved.

Supervisor

doc. RNDr. Radka Svobodová, Ph.D.

We invite enthusiastic application for a PhD position with interest in molecular biology and biochemistry. The successful candidate will work under the supervision of Dr. Krejčí to identify and characterise novel inhibitors of DNA repair nucleases, their mechanisms of action and therapeutic implications.

The PhD position candidate should hold or be about to complete a Masters degree in molecular biology, biochemistry or similar field. The applicant is also expected to demonstrate essential training in a range of molecular biology techniques relevant to basic research, should be well-organised, motivated and passionate about pursuing a career in biomedical research.

We offer fully funded positions with competitive salary in a well established laboratory. The lab hosts international team members, has a strong publication track record and international collaborations. The offered projects contribute to a rapidly advancing, very competitive field. The successful candidate can start immediately.

Supervisor

doc. Mgr. Lumír Krejčí, Ph.D.

The primary objective of our research is to delve into the collective and site-specific dynamics of both intrinsically disordered and globular proteins, with the overarching goal of elucidating their biological function and allosteric control mechanisms. Our focus lies in comprehending how knowledge of protein dynamics can inform the design of mutations within a protein to reshape its ensemble of conformational states and thereby modulate its function. Central to our investigative approach is the recognition of how evolution has shaped protein dynamics and how fundamental processes such as allosteric regulation are intricately intertwined with the dynamic coupling of different regions within an enzyme. To achieve this, we employ a combination of solution- and solid-state NMR techniques, allowing us to zoom in on the dynamic coupling mechanisms underlying allostery. Through this interdisciplinary methodology, we endeavor to gain a comprehensive understanding of how protein dynamics intersect with allosteric regulation, offering valuable insights for the development of targeted therapeutic interventions. These insights hold particular promise for addressing diseases characterized by protein dynamics and function.

Supervisor

prof. Mgr. Lukáš Žídek, Ph.D.

OBJECTIVES: The aim is to elucidate the relationship between molecular properties of amphiphilic peptides and their ability to translocate and form transmembrane pores in membranes with various lipid compositions. The obtained understanding will be used for the development of new antimicrobial peptides, which can serve as a new type of antibiotic drugs.



DESCRIPTION: Antibiotic-resistant bacteria cause more than 700 000 deaths per year, and the forecast is 10 million per year in 2050. Moreover, emerging strains of bacteria resistant to all available antibiotics may lead to a global post-antibiotic era. Because of this threat, the WHO and the UN are encouraging the research and development of new treatments. Antimicrobial peptides are promising candidates for such new treatments. We will study the molecular mechanism of action of antimicrobial peptides and determine the critical peptide properties required for membrane disruption via the formation of transmembrane pores and spontaneous peptide translocation across membranes. Based on the obtained insight, we will design new peptides and test their abilities. The most effective peptides will be evaluated for antimicrobial activity and human cell toxicity using growth inhibition and hemolytic assays, respectively. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models. The simulations will be complemented by in vitro experiments using fluorescent techniques.



EXAMPLES of potential projects: * Antimicrobial peptides and formation of membrane pores * Synergistic mechanisms between antimicrobial peptides * Membrane disruption by antimicrobial peptides in non-equilibrium conditions



MORE INFORMATION about the group: vacha.ceitec.cz



PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (robert.vacha@mail.muni.cz).

Supervisor

prof. RNDr. Robert Vácha, PhD.

Díky vysoce výkonným bioinformatickým, biochemickým a biologickým experimentálním metodikám jsou v současné době produkována extrémně velká data – např. data z kryoelektronové mikroskopie, obrazová data z nukleární magnetické rezonance nebo světelné mikroskopie, proteinové struktury generované coarse-grained simulacemi apod. Tato data jsou cenná nejen pro jejich autory, ale i pro celou vědeckou komunitu. Proto je velmi žádoucí uvedená data této vědecké komunitě zpřístupnit. Nezbytným krokem pro zpřístupnění těchto dat je jejich popis metadaty. Bez metadatového popisu by byla orientace v datech nemožná. Cílem disertační práce je vývoj metodik a workflow pro práci s těmito metadaty: jejich extrakce z (primárních) dat, popis pomocí ontologií a integrace v rámci obecnějších metadatových schémat, případně návrh systému/jazyka, který umožní s metadaty z různých zdrojů transparentně a unifikovaně pracovat.

Supervisor

doc. RNDr. Radka Svobodová, Ph.D.

Bacterial glycans, commonly found on cell surfaces, are a characteristic trait of many bacteria. They play a crucial role in adhesion, colonization, and evasion of the immune system. This Ph.D. project employs state-of-the-art molecular simulations to investigate how bacterial glycans and lipopolysaccharides interact with polymeric materials. The primary goal is to leverage molecular insights to propose innovative functionalization techniques for implant coatings, making them less prone to bacterial adherence. The student will develop and employ novel atomistic/coarse-grained models to accurately depict both bacterial glycans and polymeric surfaces. The student will master and perform multiscale molecular dynamics simulations, incorporating enhanced sampling methods such as well-tempered metadynamics and accelerated weight histogram techniques. The project will be conducted in collaboration with multiple experimental groups, enriching its practical applicability.

All interested candidates should first contact Dr. Denys Biriukov (denys.biriukov@ceitec.muni.cz)

Supervisor

Denys Biriukov, Ph.D.

Peptidová/proteinová afinita k membránám je závislá na konkrétní sekvenci a membránovém složení. Bohužel porozumění tohoto komplexního vztahu nám dosud chybí. Cílem tohoto projektu odhalit tento vztah a využít ho k vývoji nových antimikrobiálních peptidů, biomarkerů a senzorů.

Student získá znalosti v oblasti fluorescence, lipidových váčků, QCM.

Supervisor

prof. RNDr. Robert Vácha, PhD.

OBJECTIVES: The aim is to elucidate the relationship between protein sequence and preferred composition and curvature of human membranes,i.e., find peptide motifs that are selective to specific membranes in cells (plasma membrane, endoplasmic reticulum, Golgi apparatus, mitochondria, etc.). The obtained understanding will be used for the development of new protein biomarkers, sensors, scaffolds, and drugs.



DESCRIPTION: The control of biological membrane shape and composition is vital to eukaryotic life. Despite a continuous exchange of material, organelles maintain a precise combination and organization of membrane lipids, which is crucial for their function and the recruitment of many peripheral proteins. Membrane shape thus enables the cell to organize proteins and their functions in space and time, without which serious diseases can occur. Moreover, membrane curvature and lipid content can be specific to cancer cells, bacteria, and enveloped virus coatings, which could be utilized for selective targeting. We will develop a new method, using which we will elucidate the relationship between the protein sequence and the preferred membrane. The relationship will lay the foundations for the design of new protein motifs sensitive to membranes with a specific curvature and composition. Student(s) will master tools of computer simulations, in particular, molecular dynamics techniques and methods to calculate free energies. Moreover, he/she will learn the advantages and disadvantages of various protein and membrane parameterizations, including all-atom and coarse-grained models.



EXAMPLES of potential projects: * Determination of helical motifs for specific membrane compositions * Development of implicit membrane model for fast determination of protein-membrane affinity * Helical peptides and their sensitivity for membrane curvature



MORE INFORMATION: vacha.ceitec.cz



PLEASE NOTE: before the formal application process, all interested candidates should contact Robert Vacha (robert.vacha@mail.muni.cz).

Supervisor

prof. RNDr. Robert Vácha, PhD.

The research goal is investigation of structure, dynamics, and biologically relevant properties of proteins, using NMR spectroscopy and other high-resolution approaches. Currently, our group is mostly interested in studies of molecular motions using NMR relaxation and relaxation dispersion; in studies of protein disorder using NMR approaches providing sufficient resolution (usually based on non-uniformly sampled high-dimensional spectra); and in studies of interactions of intrinsically disordered proteins with their binding partners (using NMR, cryo-EM, and biophysical methods). The systems currently studied in the laboratory include bacterial RNA polymerases and microtubule associated proteins.

We are inetrested structure and dynamics of well-ordered and domains of subunits and sigma factors of RNA polymerase from B. subtilis, characterization of structural features and dynamics of disordered domain, and in importance of electrostatic interactions for structural properties and biological function of the protein. Currently we extend our interest to mycobacterial RNA polymerase.

Microtubule associated protein 2c (MAP2c) is a key factor regulating microtubule dynamics in developing brain neurons, and an example of an intrinsically disordered proteins with an important physiological function and detectable structure-function relationship. The first goal is to study MAP2c in a natural complexity and by methods providing atomic resolution. Such methods include paramagnetic relaxation interference, to detect and describe transient local structures of MAP2c important for its function, and real-time NMR, to monitor kinetics of MAP2c phosphorylation by relevant kinases of different signalling pathways. The second goal is to characterize interactions of MAP2c with biologically important binding partners, especially with isoforms and a monomeric form of regulatory protein 14-3-3. The third goal is to test the effect of cellular environment on MAP2c by recording NMR spectra at near-to-native conditions (in cells and/or cell lysates) and/or by performing cryo-electron tomography on monolayered neurons.

EXAMPLES OF POTENTIAL PHD TOPICS:

• Interactions underlying physiological function of Microtubule Associated Protein 2c
• Structure, dynamics and interactions of bacterial RNA polymerase subunits and sigma factors

Supervisor

prof. Mgr. Lukáš Žídek, Ph.D.

BACKGROUND: Several neurodegenerative diseases are associated with the formation of fibrous protein aggregates. The fibrillization of amyloid beta peptide into amyloid plaques and the agregation of hyperphosphorylated tau protein into neurofibrillar tangles are main neuropatological signs of Alzheimer disease. Studying of how different factors influence the formation of biomolecular complexes is the key for understanding underlying molecular mechanism of neurodegerative processes. The described activities are part of international research projects allowing to spend the part of PhD study at the collaborative groups in Europe or North and South America and to learn specific research techniques, there.

OBJECTIVES: The research aims to elucidate molecular mechanisms of conformational changes leading to the modified potential of biomolecular complex formation. Interdisciplinary approach combining computational biophysical chemistry, structural biology, bioinformatics and biophysical interaction techniques will be applied.

FOCUS: Doctoral research projects focus on the monitoring of post-translational modification of studied proteins, their interaction with adaptor proteins and induced conformational changes. Students benefit from outstanding research facilities of CEITEC-MU that include cryoEM tomography, NMR, AFM, and biophysical interaction methods.

EXAMPLES of potential student doctoral projects:

• Are Tau fibrils induced by phosphorylation and the interaction with 14-3-3 proteins relevant for Alzheimer disease?
• A Tau conformational changes induced by phosphorylation and 14-3-3 proteins relevant in neurodegenerative diseases
• Oligomerization states within the 14-3-3 protein family
• Computational prediction of biomolecular complexes and their statibities

MORE INFORMATION: jozef.hritz@ceitec.muni.cz

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Jozef Hritz (jozef.hritz@ceitec.muni.cz) for informal discussion.

Supervisor

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

The internal and external RNA modifications play crucial roles in a number of essential processes of eukaryotic organisms. They regulate the production of germ cells, cellular differentiation, response to stress, and defects in this pathway have been linked to a number of human diseases.

The aim of PhD projects is to study in details on how specific terminal RNA modifications regulate cellular differentiation and to study the protein-protein interactions of factors involved in the regulation of adenosine methylation (m6A) in coding and noncoding RNAs.

Prospective student should ideally have done masters in molecular biology/biochemistry and have laboratory experience in nucleic acids and/or protein purification and analysis. The most highly valued feature will, however, be excitement for science and a strong drive in tackling important biological questions.

EXAMPLES OF POTENTIAL PHD TOPICS:

• The role of posttranscriptional RNA modifications in cell differentiation
• The role of protein-protein interactions in the dynamics of m6A RNA modification

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor

MORE INFORMATION: https://www.ceitec.eu/rna-quality-control-stepanka-vanacov

Supervisor

prof. Mgr. Štěpánka Vaňáčová, Ph.D.

We apply structural biology methods in order to gain a mechanistic view of CK1ε action in the Wnt signalling pathways. CK1ε represents an attractive therapeutic target but currently two key steps in the CK1ε-mediated Wnt signal transduction are unclear: how CK1ε gets activated and/or engages target proteins in response to Wnt signal and how CK1ε phosphorylates its key substrate Dishevelled (DVL).

Our preliminary data suggest that we can efficiently apply methods of integrated structural biology to (i) probe the DVL conformational landscape using in vitro and in vivo FRET sensors coupled to SAXS and CryoEM, (ii) understand the (auto)phosphorylation regulatory mechanisms of CK1ε, (iii) analyse by NMR the functional consequences of DVL phosphorylation and (iv) monitor DVL phosphorylation by real-time NMR under controlled cellular conditions. The position is part of a multidisciplinary project that combines (i) cellular and molecular biology, (ii) proteomic analysis, (iii) biochemistry and structural biology, and received generous funding in a very competitive grant scheme.

Keywords: CK1ε, WNT, DVL phosphorylation, SAXS, cryo-EM, cryo-electron microscopy, real-time NMR

Contact:
Kostas Tripsianes, PhD | CEITEC - Central European Institute of Technology | Masaryk University | Kamenice 5/A35/1S081, CZ-62500 Brno | phone: 00420 549 49 6607

Supervisor

Konstantinos Tripsianes, Ph.D.

Our scientific goal is understanding of the most basic principles of structural dynamics, function and evolution of DNA and RNA.

To achieve our goal, we use a wide portfolio of theoretical/computational approaches. Our research is closely related to experiments, mostly via extensive collaborations, though in the prebiotic chemistry we have in house experiments. We offer thesis essentially on any topic that is currently active in the laboratory. You can get the most up-to-date idea about our current research from the WOS or SCOPUS databases, where you can find all our publications (Sponer, J.), see all our collaborators, etc. The laboratory is located at the Institute of Biophysics, Czech Academy of Sciences, Kralovopolska 135, Brno, where we have a powerfull and regularly upgraded set of high-perfomance computer clusters dedicated exclusively to our group

Our methods are:

• Classical Molecular Dynamics (MD) simulations. Besides standard simulations, we have years of experience in using all classes of enhanced-sampling techniques. We play also a prominent role in development of DNA/RNA simulation force fields and our versions are used world-wide
• Quantum-chemical (QM) method. We are using a wide spectrum of methods, ranging from ultra-accurate computations of small model systems, through large-scale QM studies on biomolecular building blocks with hundreds of atoms up to sophisticated methods that are used in studies of excited states and photochemistry; the later technique is especially relevant to study the origin of life chemistry under UV light. Again, please see the papers we have published in last years.
• Hybrid quantum-classical (QM/MM) methods, quantum molecular dynamics
• Structural bioinformatics

Specific experiments are possible in the field of prebiotic chemistry in collaborating laboratories. Modern computations are extensively combined with many experimental techniques (NMR, X-Ray, high-energy lasers, biochemical techniques) mostly via numerous collaborations. We collaborate with 30 foreign and Czech laboratories. We publish about 20 papers annually and belong to the most cited Czech research groups. We currently work in several mutually interrelated research areas.

• RNA structural dynamics, folding and catalysis
• Protein-RNA (or DNA) complexes. We try to go beyond the ensemble-averaged picture of experimental methods in order to understand how rarely accessed dynamical conformations invisible to experiments allow to separate affinity for reactivity or selectivity.
• DNA, with focus on G-quadruplexes, specifically advanced studies of quadruplex folding mechanisms
• Diverse types of quantum-chemical studies on nucleic acids systems
• Origin of life (prebiotic chemistry), i.e., creation of the simplest chemical life on our planet (or anywhere else in the Universe), with a specific attention paid to the formamide pathway to template-free synthesis of the first RNA molecules. This specific project includes also in house experimental research.

Besides studies of specific systems, we are also involved extensively in method testing/development, mainly in the field of parametrization of molecular mechanical force fields for DNA

NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact Prof. Jiri Sponer (sponer@ncbr.muni.cz) for an informal discussion.

Laboratory web page https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-acids/info-about-the-department

List of publications https://www.ibp.cz/en/research/departments/structure-and-dynamics-of-nucleic-acids/publications

Supervisor

prof. RNDr. Jiří Šponer, DrSc.

Our laboratory is focusing on study of molecular mechanisms of genome instability associated diseases
linked to DNA repair defects. DNA in cells is constantly damaged not only from external but also internal sources resulting in accumulation of hundreds of thousand lesion per cell and day. One of the mechanisms involved in genome stability is homologous recombination and its defects are linked to development of various cancers and diseases (BLM, RTS, FA, etc.).

PhD project might involved following topics: 1)RecQ4 helicase, mutated in „Rothmund-Thomson Syndrome“, a its biochemical and biological characterisation; 2) Development of new nuclease inhibitors and their preclinical characterisation; 3) Rad51 paralogs and their role in genome stability and cancer development; 4) Role of G4 structures and their metabolism in genome stability.

Our approaches involve broad range of molecular-biological, biochemical, biophysical, cell biological, genetic and structural methods.

Supervisor

doc. Mgr. Lumír Krejčí, Ph.D.

Cellular processes and external factors generate stress that can damage nuclear DNA. This includes various types of lesions that need to be recognized by the cell. Their presence must be signaled to activate a cascade of responses, including stopping the cell cycle, initiating DNA damage repair, and, as a last possibility, cell death. Our team uses a mix of cutting-edge methods, including forward genetics, genomics, bioinformatics, proteomics, modeling, and cytology, to study the process of plant DNA damage responses. Our primary models are dicot Arabidopsis thaliana and monocot Hordeum vulgare.

Notes

This work will be realized at the Institute of Experimental Botany of the Czech Academy of Sciences, Centre of Plant Structural and Functional Genomics in Olomouc.

Supervisor

doc. Mgr. Aleš Pečinka, Ph.D.

Glykoproteomika je nově vznikající obor, který odhaluje souvislosti glykoforem proteinů s rozvojem onemocnění. V organismu je až 80% všech proteinů posttranslačně modifkovaných glykosylací ovlivňující mnoho biologických procesů. Struktura glykanů a místa glykosylace na proteinu mohou být různá, čímž vznikají proteoformy s různými funkcemi, které mohou aktivovat nebo inhibovat různé buněčné procesy. Oblast glykoproteomiky tedy odhaluje tyto složité vztahy, jejich souvislosti se zdravím a nemocemi a je tedy využívána pro identifikaci dalších biomarkerů v oblasti diagnostiky nejen onkologických onemocnění.
Cílem této práce bude využití klinického materiálu (sér pacientů s definovaným onkologickým onemocněních a zdravých dárců) pro identifikaci a label-free kvantifikaci změněných glykoforem vázaných na proteinech. K tomu budou využívané proteomické analýzy založené na měření hmotnostním spektrometrem Fusion Orbitrap (Thermo Fisher Scientific). Data budou hodnocena proteomickými programy (Byonic, Peaks, Proteome Discoverer) a pomocí pokročilých statistických nástrojů v programovacím jazyku R budou definované peptidy se specifickými glykany, které jsou významné pro danou skupinu pacientů. Následně bude pomocí strojového učení hodnoceno, zda dané glykoformy peptidů pomohou zlepšit diagnostiku nebo postup v léčby onemocnění.
Doporučená literatura: (1) Fang, K., Long, Q., Liao, Z. et al. Glycoproteomics revealed novel N-glycosylation biomarkers for early diagnosis of lung adenocarcinoma cancers. Clin Proteom 19, 43 (2022). https://doi.org/10.1186/s12014-022-09376-8, (2) Kim EH, Misek DE. Glycoproteomics-based identification of cancer biomarkers. Int J Proteomics. 2011; 2011:601937. https://doi.org/10.1155/2011/601937, (3) Pan, J., Hu, Y., Sun, S. et al. Glycoproteomics-based signatures for tumor subtyping and clinical outcome prediction of high-grade serous ovarian cancer. Nat Commun 11, 6139 (2020).
https://doi.org/10.1038/s41467-020-19976-3

Supervisor

prof. Ing. Lenka Hernychová, Ph.D.

Téma zahrnuje dva studované okruhy:
A. Testování molekulárně biologických změn genomové DNA pocházející z děložní sliznice (normální, prekancerózy, nádoru) a z nebuněčné frakce periferní krve s cílem nalezení prognostického markeru.
Provedeme retrospektivní analýzu panelu molekulárně-genetických změn na základě analýzy vybraných mutací, změn počtu somatických kopií, mikrosatelitové nestability a metylace DNA u karcinomů a prekanceróz endometria
Následně ověříme prognostický význam vybraných molekulárně-biologických změn na klinickém souboru, tvořeném genomovou DNA z buněk získaných při výplachu dělohy a ctDNA z nebuněčné frakce periferní krve

B. Využití elektrodového biočipu v detekci lidského papilomaviru u prekanceróz děložního čípku s cílem vyvinout jednodušší a levnější technologii jako alternativu komerčních HPV testů
Projekt bude rozdělen do následujících okruhů:
1. výběr souboru, histologická analýza a validace komerčními HPV testy
2. příprava vhodných sond, výběr a optimalizace amplifikačních technik
3. zjednodušení a zrychlení testu a aplikace na klinický materiál.

Práce bude probíhat v moderně vybavených laboratořích RECAMO Masarykova onkologického ústavu. Napojení na grantové projekty zajištěno, možnost úvazku po domluvě se školitelem.

Supervisor

MUDr. Milan Anton, CSc.

Detection of tumor biomarkers is essential for early diagnostics of cancer, since it helps to decrease mortality and high cost associated with late treatment, and is also highly beneficial when monitoring response to therapy or possibility of relapse. In recent years, various analytical methods based on electrochemical (EC) detection have been reported. These methods have a great potential to replace standard methods which are often expensive, time-consuming, and complicated; hence, there is an urgent need to develop an affordable, simple and rapid EC  bioassays/biosensors for analysis of tumor biomarkers. The aim of this doctoral thesis is to develop and optimize bioassays for the detection of such biomarkers, mostly based on nucleic acids, i.e. DNA and RNA. The EC readout will be coupled to isothermal amplification techniques, such as LAMP, RPA or RCA, which rapidly amplify nucleic acids at constant temperatures to improve sensitivity and specificity of detection. Here is the list of selected topics anticipated to be studied in this doctoral thesis: (a) Analysis of DNA mutations in important oncogenes or tumor suppressor genes, implicated in cancer, (b) Analysis of epigenetic modifications, e.g. DNA methylation or upregulated non-coding RNAs, especially microRNAs and long non-coding RNAs, which play a major role in the carcinogenesis process, (c) Application of novel amplification techniques for detection of ultralow levels of nucleic acids, (d) Determination of circulating nucleic acids in body fluids for non-invasive diagnostics, or (e) other similar topics depending on the laboratory needs. These may include but are not limited to development of similar bioassays utilizing electrochemiluminescent (ECL) readout on electrode chips as another promising alternative, or application of third-generation Nanopore sequencing technology. The developed bioassays will be applied to biological and clinical samples and validated with standard methods. The work will be carried out in the Laboratory of Bioelectrochemistry at RECAMO, which is a part of the Masaryk Memorial Cancer Institute.

Supervisor

Mgr. Martin Bartošík, Ph.D.

Plants employ a broad spectrum of reproductive strategies, ranging from asexual species to hermaphroditism and the presence of distinct sexes. This variety significantly impacts genome architecture. Our objective is to examine plant species with varying reproductive strategies and investigate their responses to e.g. environmental changes, encompassing both biotic and abiotic stresses. Furthermore, we aim to explore the relationship between reproductive modes and genome size, genome dynamics, and ploidy levels. Our research will utilize a wide array of cutting-edge techniques in both forward and reverse genomics, including advanced microscopy and bioinformatics analyses.

Supervisor

RNDr. Roman Hobza, Ph.D.

Navrhovaný výzkum bude reagovat na potřeby současného pokroku v proteomice, glykomice a biomedicíně, který vyžaduje zavedení nových metod, které mohou přinést nové poznatky o proteinech a jejich komplexních systémech. Ve výzkumu chceme využít výhod vlastností elektrochemických přístupů k studiu proteinů a jejich komplexů na nabitých mezifázích. Plán výzkumu vychází ze současných výsledků práce v laboratoři Biofyzikální chemie a molekulární onkologie Biofyzikálního ústavu AV ČR. Budou navrženy a rozvíjeny nové elektrochemické přístupy studia biomedicínsky důležitých proteinů v komplexech s ligandy i peptidy a proteiny s cílem přispět ke stávajícím znalostem o dynamice proteinových komplexů na nabitých mezifázích. Z proteinů, budou zkoumány i glykoproteiny s cílem získání nových informací o proteinové a glykanové části intaktních a chemicky modifikovaných glykoproteinů.

Supervisor

RNDr. Veronika Ostatná, Ph.D.

Recent advances in plant genetic engineering allow precise modifications in desirable genomic region. These methodical approaches are currently employed by both basic researchers and applied biotechnologist to understand complex molecular mechanisms as well as to improve the traits of crop plants. While tools for genetic engineering, such as CRISPR/Cas9, are available for model organisms and most important economically important crops, there are still numerous plant species where precise genetic applications remain complicated or even unfeasible.

This research project will address the identification and overcoming the barriers for successful and high-throughput application of genetic engineering tools in non-model species (including Humulus lupulus, Lotus corniculatus, selected cereal crops etc).

Supervisor

Ing. Vojtěch Hudzieczek, Ph.D.

The CRISPR/Cas system is one of the most promising methods for genome editing in various organisms. In our laboratory, we developed a method for CRISPR-based genome editing in oilseed rape (Brassica napus) and Arabidopsis thaliana using hairy root cultures to study specific genes and their regulatory sequences. The PhD candidate will use molecular biology approaches to assess the functionality and efficiency of various CRISPR editing constructs, transformation methods (stable versus transient), and regeneration protocols to develop transgene-free, genome-edited plant lines in various Brassicaceae species.

Supervisor

RNDr. Veronika Jedličková, Ph.D.

Jak jsou chromozomy organizovány a uspořádány v buněčném jádru? Něco málo víme, ale víc toho nevím, ani po více než 100 letech výzkumu v této oblasti. Disertační práce je zaměřena na analýzu konfigurace interfáznich chromozomů, jejich domén (např. centromery, telomery) a tzv. chromosome territories v jádrech rostlin se sekvenovým genomem z různých fylogenetických skupin. Cílem projektu je pochopení evolučních trendů a zákonitostí organizace chromatinu a chromozomů v interfázních jádrech rostlinných druhů. K zodpovězení těchto otázek budou využity metody molekulární cytogenomiky a imunocytologie (např. FISH, malování chromozomů oligo- malovacími sondami, protilátky proti kinetochorovým a CENH3 proteinům), a srovnávácí genomiky založené na celogenomovém sekvenování (např. kontaktní Hi-C a Pore-C interaktomy). Metodicky práce zahrnuje tři základní okruhy: (1) identifikace unverzálních a chromosomově-specifických DNA a proteinových sond s použitím sekvenovaných genomů, (2) lokalizace těchto sond na chromozomech a v interfázních jádrech (3D imuno/FISH), a (3) analýza a interpretace dostupných 3D genomických dat (sekvenované genomy) a jejich interpretační srovnání s cytogenomickými daty. Vzhledem k výzkumnému zaměření VS M. Lysáka lze předpokládat, že výše uvedené metodické přístupy budou preferenčně aplikovány u druhů čeledi Brassicaceae (brukovovité). Konzultant: Dr. S. Grob (IBMP Strasbourg).

Supervisor

prof. Mgr. Martin Lysák, Ph.D., DSc.

We will utilize machine learning techniques such as deep neural networks to identify, analyze and interpret functional genomic segments.

The transcription and translation of genes can be crucially influenced by regulatory elements such as enhancers, silencers, insulators and tethering elements. Gene regulatory elements are possible drivers of many diseases, from leucemia to diabetes.

While those regulators are well mapped and annotated for human genome and some frequently used model organisms; the declining cost of DNA sequencing comes with new diverse genomic datasets for animals and plants where such annotations are not known. Unsupervised neural networks like autoencoders and supervised methods like transformers can take advantage of a vast amount of data and discover similarities and new insights without the need of hand-crafted features.

Because of the black-box nature of neural networks, the special care should be devoted to understanding the data and interpretability of the models.

Supervisor

Mgr. Petr Šimeček, MSc., Ph.D.

Our workgroup is interested in molecular basis of severe dyslipidemias in human. The most common of dyslipidemias is familial hypercholesterolemia (FH). The frequency of FH in most populations is about 1/200, and so it is possible to predict that about 50,000 people could be affected in the Czech Republic. The clinical phenotype of FH is caused predominantly by mutations in the LDLR gene. LDLR mutations have been reported along the whole length of the gene. Our workgroup focuses on functional assays of LDLR mutations. For further details please refer to our publications (PMIDs: 27175606, 20663204, 28379029, …).

Supervisor

Mgr. Lukáš Tichý, Ph.D.

Proteomická analýza je jedním z klíčových faktorů umožňujících zásadní pokrok našeho poznání nejen v oblasti molekulární biologie a biochemie. Proteomická analýza je souborem jednotlivých kroků zahrnujících přípravu vzorku, jeho vlastní analýzu, převážně s využitím hmotnostní spektrometrie (MS), zpracování naměřených dat, jejich statistické hodnocení a bioinformatickou analýzu, přičemž každý z kroků má zásadní vliv na kvalitu získaných výstupů. Cílem disertačních prací v rámci tohoto výzkumného zaměření bude vývoj nových postupů, zejména v oblasti přípravy různých typů vzorků před MS analýzou, resp. vývoj postupů pro zpracování MS dat umožňujících podrobnější charakterizaci analyzovaného vzorku. Studenti budou mít přístup k nejmodernější MS instrumentaci a možnost zapojení do projektů VS Proteomika (CEITEC MU) i spolupracovat s výzkumnými týmy v rámci MU i mimo ni.

Notes

Před podáním přihlášky je nutno se neformálně seznámit s tématem, kontaktujte prof. Zbyňka Zdráhala.

Supervisor

prof. RNDr. Zbyněk Zdráhal, Dr.

Genomy eukaryot nejsou neměnnými genetickými entitami. Zejména v poslední době se stále silněji ukazuje, že se jedná o velmi dynamické systémy, generátory vlastních přestaveb, schopné citlivě reagovat na změny prostředí. Většina eukaryotních genomů je z velké části tvořena opakujícími se úseky DNA, tzv. repeticemi. Mezi repetice patří i klíčoví hráči dynamiky genomů - transponovatelné elementy, tzv. transpozony, populárně označované jako „skákající geny“. Transpozony jsou rozptýleny po celém genomu. Přestože transpozony představují významnou část rostlinných genomů, jejich evoluční dynamika a vliv na fungování buňky začínají být teprve chápány.

V rámci navrhované dizertace budeme pomocí bioinformatických nástrojů i experimentů studovat různé aspekty života transpozonů v rostlinných genomech - jejich věk, strukturní rysy, vlny amplifikací, rozsah genové konverze a ektopické rekombinace stejně jako vliv těchto procesů na velikost genomů a účast při tvorbě centromer a formování 3D organizace interfázního jádra. Naše výsledky přispějí k pochopení struktury, funkce a evoluce transpozonů. Doktorská práce předpokládá zvládnutí širokého spektra metod molekulární biologie a genomiky a také řady bioinformatických nástrojů a rovněž práci s odbornou literaturou. Pro bioinformatické analýzy budou využita jak data z dostupných databází, tak i naše vlastní data pocházející ze sekvenování druhé generace (NGS). Student bude používat nejrůznější bioinformatické nástroje dostupné na internetu i vlastnoručně vytvořené. Výsledky analýz budou publikovány v kvalitních impaktovaných časopisech. Pro studenta nabízíme možnost pracovního úvazku. Projekt je financován Grantovou agenturou ČR.

Supervisor

doc. RNDr. Eduard Kejnovský, CSc.

Genome sequencing brings a huge amount of information regarding the genetic basis of life. While this information provides a foundation for our understanding of biology, it has become clear that the DNA code alone does not hold all the answers. Epigenetic modifications and higher order DNA structures beyond the double helix contribute to basic biological processes and maintaining cellular stability. Local alternative DNA structures are known to exist in all organisms. Negative supercoiling induces in vitro local nucleotide sequence-dependent DNA structures such as cruciforms, left-handed DNA, triplex and quadruplex structures etc. The formation of cruciforms requires perfect or imperfect inverted repeats of 6 or more nucleotides in the DNA sequence. Inverted repeats are distributed nonrandomly in the vicinity of breakpoint junctions, promoter regions, and at sites of replication initiation. Cruciform structures could for example affect the degree of DNA supercoiling, the positioning of nucleosomes in vivo, and the formation of other secondary structures of DNA. The three-dimensional molecular structure of DNA, specifically the shape of the backbone and grooves of genomic DNA, can be dramatically affected by nucleotide changes, which can cause differences in protein-binding affinity and phenotype. The recognition of cruciform DNA seems to be critical not only for the stability of the genome, but also for numerous, basic biological processes. As such, it is not surprising that many proteins have been shown to exhibit cruciform structure-specific binding properties [1] or G-quadruplex binding properties [2]. Contemporary we have developed easy accessible web tools for analyses of inverted repeats [3] and G-quadruplexes[4] and we have analyzed the presence of inverted repeats and G-quadruplexes in various genomic datasets, such as all sequences mitochondrial genomes [5], all bacterial genomes [6], in S.cerevisiae (in review), in human genome etc. A deeper understanding of the processes related to the formation and function of alternative DNA structures will be an important component to consider in the post-genomic era.

Supervisor

prof. Mgr. Václav Brázda, Ph.D.

Telomeres are the physical ends of linear chromosomes that protect these ends against erroneous recognition as unrepaired chromosomal breaks and regulate the access to Telomerase, a reverse transcriptase that solves the problem terminal DNA loss in each cell cycle. Telomeric structures are known to be composed of short repetitive DNA sequences (telomeric repeats), histone octamers, and number of proteins that bind telomeric DNA, either directly or indirectly, and together, form the protein telomere cap.

Interestingly, telomeric repeats are not exclusively located at the chromosome ends, but they belong among cis-regulatory elements present in promoters of several genes. The distribution of short telomeric motifs (telo-boxes) within the genome is not random, and proteins associated with these telomeric repeats may serve as the epigenetic regulatory mechanisms facilitating metastable changes in gene activity.

The telomeric cap proteins of diverse organisms are less conserved than one might expect. In plants, knowledge of telomere-associated proteins associated with telomeres and regulation of access to telomerase complex is incomplete. The research aims to elucidate the roles of candidate proteins involved in telomerase biogenesis in plants. The outcomes contribute to the characterization of new telomere- or telomerase-associated proteins, complete our knowledge of telomerase assembly or telomere maintenance in plants. In addition, we would like to examine the regulatory factors associated with the telo-boxes present in promoters of the genes active during plant development.

Notes

Poznámky: Práce může být vypracována ve slovenštině či angličtině.

Supervisor

doc. Mgr. Petra Procházková Schrumpfová, Ph.D.

Histone sequence variants and their post-translational modifications (PTMs) are epigenetic marks that significantly influence a number of processes, including the cell cycle and protein interactions. The diversity of histones and the complexity of their modifications in amino acid sequences make histone characterization challenging. The aim of this research is to develop and refine methodologies for the characterization of histone variants and PTMs for mass spectrometry analysis, which will subsequently be used in projects focused on epigenetic regulation in plants, mammals and humans. Epigenetic changes in histones will be investigated in the context of proteome of related cellular signaling pathways.

Supervisor

Mgr. Gabriela Lochmanová, Ph.D.

Posttranslační modifikace (PTM) významně ovlivňují regulaci buněčných procesů. V současné době je známo více než 400 druhů. Analýza PTM je poměrně složitý proces, jelikož neexistuje jedna univerzální metoda, která by byla schopná detekovat všechny druhy PTM současně, a zpravidla je nutno použít pro každý druh modifikace individuální postup přípravy vzorku, resp. metodu analýzy. Navíc modifikovaných forem proteinů je v rámci proteomu kvantitativně řádově méně než odpovídajících nemodifikovaných proteinů, což také znesnadňuje jejich detekci.

Cílem disertační práce bude vývoj a optimalizace souboru metod pro kvalitativní a kvantitativní charakterizaci vybraných typů posttranslačních modifikací hmotnostní spektrometrií a aplikace těchto metod v rámci řešení probíhajících projektů.

Experimentální část bude probíhat v laboratořích VS/CL Proteomika, CEITEC-MU (budova E26, UKB Bohunice), vybavených špičkovou instrumentací.

Notes

Před podáním přihlášky je nutno se neformálně seznámit s tématem, kontaktujte prof. Zbyňka Zdráhala.

Supervisor

prof. RNDr. Zbyněk Zdráhal, Dr.

Our lab is interested in the chromatin structure and dynamics. The chromatin structure must be not only maintained through the cell cycle, but also dynamically modulated during processes like mitosis and replication. Amongst the chromatin-associated complexes, the SMC (Structural Maintenance of Chromosomes) complexes play the central role. Two of them, Cohesin and Condensin, facilitate chromosome segregation and condensation, respectively. Third, the most enigmatic SMC5/6 complex is involved in the DNA damage repair and replication restart, however its essential chromatin-modulating function is still unclear. Our laboratory focuses on the SMC5/6 architecture and functions using state-of-the-art structural biology approaches and various molecular biology tools. For further details please refer to our website (http://www.ncbr.muni.cz/SPEC/) and our publications (https://orcid.org/0000-0002-6223-5169).

Supervisor

doc. Mgr. Jan Paleček, Dr. rer. nat.

Supervisor

doc. RNDr. Miroslav Fojta, CSc.

In brief, intracellular life of telomerase is linked to processes of telomerase biogenesis, action at telomeres and degradation. During these processes telomerase interacts with many protein partners that might be essential for particular steps. Highly dynamic nature of telomerase interactome causes difficulty in uncovering functions of telomerase partners that are important for telomerase and those unrelated to telomerase. Using classical experimental methods as well as genomics and proteomics approaches accompained with in silico analyses, we study structure-functional relationship of telomeres and telomerases.

Supervisor

Mgr. Eva Sýkorová, CSc.

Diabetické onemocnění ledvin (DKD) je závažnou komplikací diabetes mellitus, s výrazným zaměřením výzkumu na buňky proximálního tubulu (PTEC), jejichž dysfunkce je klíčová v patogenezi DKD. Tyto buňky jsou zvláště citlivé na mitochondriální dysfunkci kvůli vysoké energetické potřebě. V léčbě DKD se významně prosazují nové terapeutické přístupy, především metformin a SGLT2 inhibitory jako empagliflozin, jež mají výrazný renoprotektivní efekt. Hlavním cílem této práce je zkoumání vlivu metforminu a empagliflozinu na proteinovou a genovou expresi enzymů energetického metabolismu v buňkách HK-2, reprezentujících PTEC, v normo a hyperglikemickém prostředí, pro hlubší porozumění jejich působení v kontextu DKD.

Supervisor

Mgr. Katarína Chalásová, Ph.D.

The project will focus on studying the Adar mutant mice that lack the dsRNA RNA editing enzyme, Adar1. Adar null mutant mice die as embryos and embryonic lethality is rescued to live birth in Adar, Mavs double mutants that also lack a key innate immune sensor protein that is activated by unedited dsRNA. However, these double mutant mice die within a few weeks with massive intestinal cell death. To improve this rescue, we have crossed in mutations removing other innate immune sensors.
Adar, Mavs, Eif2ak2 triple mutant mice that also lacking the dsRNA-activated activated PKR sensor protein further improve the rescue, sixty percent of these triple mutant mice live beyond the first month and have apparently normal lifespans. The project is to cross in various other mutants to reduce cell death, such as Trp53 and Caspase11, to see if these extend survival of Adar, Mavs double mutants. We may cross in further mutations affecting sensors, such as the Z-RNA sensor protein ZBP, to see if there is further improvement in this rescue.
We also have another set of mouse strains starting from AdarE912A which expresses a deaminase-inactive mutant and shows mutant phenotypes similar to Adar null mutant but less severe. AdarE912A, Ifih1 double mutants lacking the Mda5 dsRNA sensor protein activating the Mavs signaling pathway are fully viable, with normal lifespans. However, we have discovered that small size and early death in of pups is merely delayed to the next generation in this strain; possibly the mothers have some inflammation that is harmful to their offspring. The student will examine these AdarE912A, Ifih1 second generation mutants to see if they have the same defects as first-generation Adar, Mavs double mutants.
Finally, another part of the project is to analyze the Adar mutant phenotypes in brain. In humans, ADAR mutants cause an encephalopathy called Aicardi Goutières Syndrome, which involves aberrant interferon expression and gives symptoms that mimic symptoms of congenital virus infection.

Supervisor

prof. Mary Anne O'Connell, PhD.

This research direction includes the structure, evolution and maintenance of telomeres and their roles in chromosome stability, DNA repair and plant speciation. A special attention is given to characterisation of telomerase components and interactors.
Further, we investigate epigenetic mechanisms in the regulation of gene expression, chromatin assembly, genome stability and telomere homeostasis. Biochemical, bioinformatic and molecular biology approaches are applied in this research. As model systems, we primarily use plants and plant cell cultures.
For more details, see our web pages: https://www.ceitec.eu/chromatin-molecular-complexes-jiri-fajkus/rg51

Supervisor

prof. RNDr. Jiří Fajkus, CSc.

Interestingly, we have recently observed a widespread link between homologous recombination (HR) and gene silencing. Though we now know that mutations of HR genes lead to upregulation of transcription of various genes in the S. pombe model organism, the underlying mechanisms remain largely unclear. In this research direction, we plan to investigate the relationship between HR and transcription in detail using molecular biology, bioinformatic, and biochemical approaches. We aim to determine where, when, and how the HR-dependent effect on transcription occurs. To reach this goal, we will use genome-wide NGS approaches, RT-qPCR, site-specific yeast assays, and map the involved interactions at the molecular level. Although this research aims to gain insight into the relationship between HR and gene silencing in fission yeast, the strong similarities between the key molecular mechanisms of S. pombe and humans make it highly likely that the identified processes are shared by both species and may be utilized in human therapy in the future.

Supervisor

Mgr. Peter Kolesár, Ph.D.

Notes

Před podáním přihlášky je vhodné se seznámit s konkrétními tématy pro daný kalendářní rok. Kontakt: doc. Hrstka, MOÚ, Brno.

Supervisor

doc. Mgr. Roman Hrstka, Ph.D.

Annotation: 

This Ph.D. project is part of a national initiative to build a cutting-edge platform for storing and analyzing omics data, spanning genomic, epigenomic, transcriptomic, and proteomic datasets. The platform will be integrated with European networks created through the Genomic Data Infrastructure (GDI) project, enabling the sharing and analysis of data across borders, granting access to vast amounts of multi-omics data. This level of collaboration requires a federated approach, where data remains at local nodes, while computation and model training happen across distributed systems, ensuring both data privacy and security.

The primary goal of this Ph.D. will be to develop and orchestrate bioinformatics tools that leverage federated learning. These tools will facilitate scalable, collaborative computation across multiple European institutions, allowing local nodes to train models independently and contribute to a global model without centralized data storage. The Ph.D. candidate will design and deploy these federated bioinformatics tools, focusing on integrating long-read sequencing technologies - emphasizing the detection of structural variants and modeling methylation patterns - along with short-read sequencing data for a comprehensive analysis.

Federated learning will be crucial for efficiently processing the distributed datasets, allowing the platform to securely compute over sensitive data while preserving its informative value. By developing novel algorithms and workflows that integrate federated computing with omics data, the Ph.D. candidate will push the boundaries of current bioinformatics approaches. The research will lead to first-author publications, making significant contributions to both national and European scientific advancements in genomics, epigenomics, and multi-omics data integration.

Requirements for candidate:
The ideal candidate should possess strong IT skills, particularly in coding, machine learning, and data science, with a solid understanding of bioinformatics. Experience with sequencing data analysis, especially long-read and short-read technologies, is highly advantageous. Familiarity with federated computing concepts is also a plus.
PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
 

Recommended literature:

1.Zhao, Y., et al. “Federated Learning with Non-IID Data.” Proceedings of the 22nd International Conference on Artificial Intelligence and Statistics (2018).

2. Li, T., et al. “Federated Optimization in Heterogeneous Networks.” arXiv preprint arXiv:1812.06127 (2018).

3.Celi, L. A., et al. “Federated Learning Applications in Medicine: A Systematic Review.” PLOS Digital Health (2022).

4.Rieke, N., et al. “The Future of Digital Health with Federated Learning.” Nature Medicine 26 (2020): 1691–1700.

5.Wang, S., et al. “Privacy-Preserving Federated Learning for Bioinformatics Data Integration.” IEEE Transactions on Big Data (2022).

Supervisor

Mgr. Vojtěch Bystrý, 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).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340

Notes

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

Supervisor

Konstantinos Tripsianes, Ph.D.

Annotation:
The project is focused on detailed structural characterization of short oligonucleotides in noncanonical forms clipped together by proper sequential motifs. 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 a deeper understanding of key interactions that contribute to the system folding and stability.

Requirements for candidate:
Structural chemistry or biology, advanced NMR spectroscopy, computational chemistry

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
 

Recommended literature:

Aleš Novotný, Jan Novotný, Iva Kejnovská, Michaela Vorlíčková, Radovan Fiala, 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.

Supervisor

prof. RNDr. Radek Marek, Ph.D.

Annotation:

With nearly 10 million lives claimed annually, cancer remains one of the leading causes of mortality worldwide, highlighting the urgent need for more effective treatments. One promising strategy involves mRNA-based cancer immunotherapy vaccines, which require a drug delivery system capable of reliably reaching the cytosol. Developing such delivery systems is challenging: they must ensure cytosolic delivery and therapeutic efficacy while maintaining safety, long-term stability, and compliance with scalable manufacturing standards -  including high mRNA loading efficiency and uniform particle size. Current lipidand polymer-based systems offer distinct advantages but integrating lessons from both may help develop more effective next-generation carriers. A major limitation remains the incomplete understanding of nanoparticle assembly and disassembly under diverse physiological conditions (e.g., extracellular fluids, endosomal compartments, cytosol). This project will use coarse-grained molecular simulations, complemented by in-house experimental validation, to gain molecular insights in the controlled system assembly and disassembly. Our goal is to guide the rational design of improved mRNA delivery systems to advance the efficacy of cancer immunotherapy.

Requirements for candidate:
 
Msc in computational biophysics/chemistry/physics and related fields
Experience with Molecular Dynamics using coarse grained or atomistic models
Advantage is experience with simulations of disordered proteins/polymers and membranes
Excellent track record
Good English language – spoken and written
Motivated person with collaborative mind set

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340


Recommended literature:

Paunovska K., et al.: Nat Rev Genet 2022, 23, 265–280, Doi: 10.1038/s41576-021-00439-4
Hou X., et al.: Nat Rev Mater 2021, 6, 1078–1094, Doi: 10.1038/s41578-021-00358-0
Yasuda I. et al.: J. Chem. Theory Comput. 2025, 21, 5, 2766–2779, Doi: 10.1021/acs.jctc.4c01646
Chew P.Y., et al.: Chem. Sci., 2023,14, 1820-1836, Doi: 10.1039/D2SC05873A

Supervisor

prof. RNDr. Robert Vácha, PhD.

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).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
 

Notes

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.

Supervisor

prof. MUDr. Mgr. Marek Mráz, Ph.D.

Annotation: 
Co-translational quality control is triggered as a response to translational stalling events. Yet, different molecular mechanisms are employed for the recognition of these stalls and to trigger downstream rescue and quality control pathways. The use of collided ribosomes as a proxy for the recognition of translation problems in the cell is conserved from bacteria to humans. In eukaryotes, co-translational quality-control processes triggered by ribosome collisions accomplish several tasks and eventually trigger stress response signalling pathways. These tasks include the degradation of aberrant mRNAs, the degradation of potentially deleterious nascent peptides, the ribosomal subunit rescue and tRNA recycling. We mainly use structural analysis by cryo-EM to gain mechanistic understanding of these translational control events. To that end, we reconstitute macromolecular complexes involved in these processes in vitro or isolate them from cells.
The successful candidate will utilize a multidisciplinary approach to provide detailed mechanistic understanding of the critical human co-translational processes. 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 for candidate:
The ideal candidate should have background in either molecular biology, biochemistry or structural biology. Experience with human cell culture work, RNA biochemistry or protein expression and purification is a strong plus.

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340

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.
 

Supervisor

RNDr. Petr Těšina, Ph.D.

Annotation: 
 
Protein-DNA interactions are critical in cellular processes and genetic instability-related conditions, particularly involving G-quadruplexes (G4) and their complementary C-rich sequences (i-Motif). Due to the composite viscoelastic environment in living cells, the polymorphism is highly complex, featuring dynamic conformational equilibrium between several folded and unfolded sub-populations driven by G4/i-Motif-binding proteins (Helicases, recruited proteins, transcription factors, etc.). Helicases are ubiquitous molecular motors involved in the homeostatic regulation of the folding/unfolding of these structures, thereby mediating replication, repair, transcription, and DNA damage response through protein barriers. Peptides from helicase motifs can be used to investigate atomistic details of G4-Helicase interactions and decipher structure-activity relations. The candidate will explore the folding and regulation of their rugged folding energy landscape of G-quadruplexes and i-Motifs in the presence of peptide fragments from the helicase motifs.
This project will utilize low and high-resolution orthogonal biophysical techniques (such as NMR, native mass spectrometry, and molecular dynamics) to investigate atomistic details of these interactions and conformational alterations. The results will shed light on the fundamental mechanisms of Helicase-Non-canonical nucleic acid interactions, which are essential for understanding G4/ i-Motif biology in fine-tuning gene expression and alleviating associated cellular dysfunctions. The design of peptide-based G4/i-Motif inhibitors can be used in (a) epigenetic-driven anticancer, neurological, or antiviral therapies by disrupting the overrepresentation of those forms, (b) non-invasive biomarkers to detect G4/i-Motif structures in biological samples (blood plasma) for disease diagnosis.

Requirements for candidate: Master's degree in Chemistry/Biochemistry/Biology/Biophysics

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340

Recommended literature:

1. Tateishi-Karimata,H. and Sugimoto,N. (2021). Nucleic Acids Res., 49, 7839–7855.
2. 17. Sauer,M. and Paeschke,K. (2017. Biochem. Soc. Trans., 45, 1173–1182.
3. Mendoza,O., Bourdoncle,A., Boulé,J.-B., Brosh,R.M. and Mergny,J.-L. (2016). Nucleic Acids Res., 44, 1989–2006.
4. Chen,M.C., Tippana,R., Demeshkina,N.A., Murat,P., Balasubramanian,S., Myong,S. and Ferré-D'Amaré,A.R. (2018). Nature, 558, 465–469.
5. Heddi,B., Cheong,V.V., Martadinata,H. and Phan,A.T. (2015). Proc. Natl. Acad. Sci., 112, 9608–9613.

Supervisor

doc. Mgr. Lukáš Trantírek, Ph.D.

Annotation: 
In-cell NMR spectroscopy has emerged as a unique and powerful approach for probing biomolecular structure, dynamics, and interactions directly within living human cells under near-physiological conditions. It holds transformative potential for both basic biomedical research and pharmaceutical development, enabling direct analysis of drug-target engagement, binding affinities, and structural validation in the cellular context. However, current applications of in-cell NMR remain largely confined to asynchronous, 2D monocultures of immortalized or cancer-derived cell lines. This narrow experimental window limits both biological relevance and translational potential.
In our previous work, we successfully addressed key limitations of in-cell NMR by establishing two innovative strategies: (1) structural characterization in cell cycle–synchronized cells and (2) in-cell NMR within 3D human tissue spheroids. These efforts provided essential proof-of-principle for expanding the applicability of the technique to more complex biological systems.
Building on this foundation, the proposed project aims to take a critical step forward by developing and applying in-cell NMR spectroscopy in 3D human organ models derived from pluripotent stem cells. These models represent the current gold standard for replicating organ-level physiology in vitro, offering unprecedented opportunities to study molecular events within realistic tissue architecture and differentiation contexts. The PhD candidate will develop protocols for isotope labeling, sample handling, and NMR acquisition in stem cell-derived 3D tissues.

Requirements for candidate:

Master's degree in Molecular or Cellular Biology/ Biochemistry /Chemistry / Biophysics

Prior experience with organoid production, induced pluripotent stem cells (iPSCs), or protein NMR spectroscopy is considered an asset.

PLEASE NOTE: Before starting the formal application process, applicants must register on the CEITEC PhD School website (link).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340

Recommended literature:
1: Theillet FX, Luchinat E. In-cell NMR: Why and how? Prog Nucl Magn Reson
Spectrosc. 2022 Oct-Dec;132-133:1-112.
2: Theillet FX. In-Cell Structural Biology by NMR: The Benefits of the Atomic
Scale. Chem Rev. 2022 May 25;122(10):9497-9570.
3: Luchinat E, Banci L. In-cell NMR: From target structure and dynamics to drug
screening. Curr Opin Struct Biol. 2022 Jun;74:102374.
4:  Rynes J, Istvankova E, Dzurov Krafcikova M, Luchinat E, Barbieri L, Banci L,
Kamarytova K, Loja T, Fafilek B, Rico-Llanos G, Krejci P, Macurek L, Foldynova-
Trantirkova S, Trantirek L. Protein structure and interactions elucidated with
in-cell NMR for different cell cycle phases and in 3D human tissue models.
Commun Biol. 2025 Feb 7;8(1):194.

Supervisor

doc. Mgr. Lukáš Trantírek, Ph.D.

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).
More information:
https://www.ceitec.eu/admission-step-by-step/t11340
 

Notes

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.

Supervisor

prof. MUDr. Mgr. Marek Mráz, Ph.D.