Dissertation Thesis

We offer a wide range of dissertation topics. If you do not find the right one, please do not hesitate to contact the appointed supervisors, research group leaders or individual researchers. Suitable inspiration may come from dissertations that have already been defended.

Topics

Structure of non-canonical forms of DNA
Supervisor: prof. RNDr. Radek Marek, Ph.D.

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.

Analysis of protein families structure
Supervisor: doc. RNDr. Radka Svobodová, 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.

Bioinformatics workflows for management of experimental data
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.

Computational Modelling of Therapeutically Relevant Biomolecular Systems
Supervisor: RNDr. Petr Kulhánek, 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 and electron microscopy of transcription condensates
Supervisor: prof. Mgr. Richard Štefl, 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.

Inhibition of DNA repair nucleases – from biological probe to cancer therapy
Supervisor: doc. Mgr. Lumír Krejčí, 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.

Investigating the Protein Dynamics, Interactions and Allostery for Therapeutic Applications
Supervisor: prof. Mgr. Lukáš Žídek, 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.

Mechanism of action of antimicrobial peptides
Supervisor: prof. RNDr. Robert Vácha, PhD.
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.

Metadata for annotation of experimental data in life sciences
Supervisor: doc. RNDr. Radka Svobodová, Ph.D.

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.

Molecular Signature of Bacteria Attachment to Functionalized Surfaces
Supervisor: Denys Biriukov, 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.

Peptide selectivity for lipid membranes
Supervisor: prof. RNDr. Robert Vácha, PhD.

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.

Protein Affinity and Selectivity to Cellular Membranes
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.

Protein Structure and Dynamics
Supervisor: prof. Mgr. Lukáš Žídek, Ph.D.

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.

Proteins structure alteration and their involvement in complex formation relevant for neurodegenerative disease.
Supervisor: doc. RNDr. Mgr. Jozef Hritz, 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.

RNA Quality Control
Supervisor: prof. Mgr. Štěpánka Vaňáčová, 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.

Structural biology of WNT signalling
Supervisor: Konstantinos Tripsianes, 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.

Structural dynamics, function and evolution of RNA and DNA. From the origin of life to modern biochemistry and structural biology.
Supervisor: prof. RNDr. Jiří Šponer, DrSc.

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.

Study of molecular details of DNA repair and its role in cancer
Supervisor: doc. Mgr. Lumír Krejčí, Ph.D.

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.

Application of Glycoproteomics in Cancer Diagnostics
Supervisor: prof. Ing. Lenka Hernychová, 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.

Application of tumour biomarkers in gynecological precancer diagnostics
Supervisor: MUDr. Milan Anton, CSc.

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.

Bioelectrochemistry in molecular oncology
Supervisor: Mgr. Martin Bartošík, Ph.D.

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) or electrochemiluminescence (ECL) 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 or ECL 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. 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 upregulated non-coding RNAs, especially microRNAs and long non-coding RNAs, which play a major role in the carcinogenesis process, (c) Analysis of DNA methylation as an important epigenetic modification, (d) Application of novel amplification techniques for detection of ultralow levels of nucleic acids, (e) Determination of circulating nucleic acids in body fluids for non-invasive diagnostics, or (f) other similar topics depending on the laboratory needs. 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.

DNA damage repair of DNA-protein crosslinks in Arabidopsis thaliana
Supervisor: doc. Mgr. Aleš Pečinka, Ph.D.

Cellular processes and external factors generate stress that can damage nuclear DNA. Proteins covalently bound to DNA represent a little-studied but serious type of DNA damage – DNA-protein crosslinks (DPCs). DPCs block transcription and DNA replication and therefore need to be repaired. We have developed a highly efficient genetic screen for the identification of genes involved in DPC repair. Using the candidates from this genetic screen, we aim to reconstruct molecular pathways protecting the plant genome against DPCs. This will help to understand an important mechanism ensuring plant fitness and fertility.

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.

Dynamics of genomes in plants with different reproductive strategies
Supervisor: RNDr. Roman Hobza, 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.

Effects of the heat stress on DNA damage repair efficiency in plants
Supervisor: Mgr. Martina Dvořáčková, Ph.D.

Heat stress is a worldwide environmental constraint for plants, impairing their growth and fertility and representing a compelling issue in agriculture. While short-term fluctuations of temperature may be tolerated, the long-term cultivation of plants at suboptimal conditions causes the systemic reaction with severe consequences on plant cellular physiology. Our research focuses on examining the DNA damage response in the model plant Arabidopsis thaliana, along with other alternative plant models, specifically assessing the immediate effects of heat stress on DNA damage factors. A key aspect of our study is observing the liquid-liquid phase separation that facilitates the assembly of DNA repair mechanisms during heat exposure. In addition to these reparative processes, we aim to explore changes induced by heat stress in the nuclear structure, chromatin remodeling, and the nuclear proteome. Our methodologies include traditional genetic, biochemical, and microscopy techniques, such as laser-microirradiation and live-cell imaging, which are crucial for in vivo observation of these reparative processes.

Supervisor

Mgr. Martina Dvořáčková, Ph.D.

Electrochemical investigation of biomedically relevant proteins and their interactions.
Supervisor: RNDr. Veronika Ostatná, 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.

Exploring of glycosylation towards diagnosis and prognosis of malignancies via mass spectrometry-based approaches.
Supervisor: RNDr. Erika Lattová, PhD.

Glycosylation as one of the major posttranslational modification (PTM) of proteins is involved in a wide range of fundamental molecular processes. Variations in oligosaccharide (glycan) structures have been also shown in association with different pathological events. Glycans are extraordinarily complex molecules and unlike other oligomers, they are synthesized through interaction with a complex biochemical environment comprising hundreds of glycosyltransferases. Consequently, glycans possess significant structural heterogeneity. In addition, proteins may carry several different glycans, displaying a wide range of site occupancy, which could dynamically change. These facts make investigation of oligosaccharides rather demanding and usually require the sequential employment of several approaches. On the other hand, the above-mentioned characteristics make glycans particularly attractive candidates in medical studies.
Although a number of methods have been developed for identification of glycans, the investigation of glycoconjugate structures and understanding their roles in living systems represents tremendous challenges in the field of proteomics. Mass spectrometry (MS) is one the most sensitive and fast technique for the analysis of biomolecules. The information gained by MS allows to assign putative monosaccharide structures present in detected glycans since the mass of a monosaccharide is measured with a high degree of accuracy. Moreover, tandem MS experiments enable more detailed information and in conjunction with oligosaccharide dissection using exoglycosidase enzyme arrays can provide structural analysis and confirm the types of linkages. Therefore, one of the crucial tasks of the thesis will be the investigation of glycosylation in association with pathological events employing MS based proteomic methodology. Experimental work will be performed in laboratories of RG and CF Proteomics, CEITEC, building E26.

Lattová E., Skřičková J., Hausnerová J., Frola L., Křen L., Zdráhal Z., Bryant J., Popovic M. Ihnátová I.:
N-Glycan profiling of lung adenocarcinoma in patients at different stages of disease
Mod. Pathol., 33 (6), 1146-1156 (2020)

Notes

It is necessary to contact Dr. Lattova (or prof. Zdrahal) for informal introduction of the topic before a formal application.

Supervisor

RNDr. Erika Lattová, PhD.

Genetic engineering for non-model plants
Supervisor: Ing. Vojtěch Hudzieczek, 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.

Chromosome organisation in interphase plant nuclei
Supervisor: prof. Mgr. Martin Lysák, Ph.D., DSc.

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.

Identification and Analysis of DNA Functional Elements Using Deep Neural Networks
Supervisor: Mgr. Petr Šimeček, MSc., Ph.D.

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.

Identification of novel molecular components involved in root directional growth.
Supervisor: Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Young seedlings when germinating have at least two key tropic responses to execute, that is reorient the shoot part toward the energy giving light and re-align the root with the gravity vector to be able to grow into the soil that contains moisture and vital minerals. In the case of the root there are more levels of developmental complexity to be taken into consideration as it grows into the mature root system. While the key principles of auxin role in gravitropism have been worked out, the fine-tuning of auxin transport as well as the interlink between auxin and modifications of gravitropic sensing are still not fully understood, and that knowledge gap we want to supplement with this project.
Within this project we plan to address the molecular mechanism(s) underlying the root directional growth as well as how gravitropic sensing is linked and also unlinked with auxin transport enabling main root and lateral roots gravitropism modifications. We will perform gravity sensing-based forward genetic screen to uncover novel molecular regulators involved in gravity perception and execution. Next we will map obtained mutants and characterize physiological and cellular phenotype of mutants and overexpression lines.

Supervisor

Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Mechanisms of effect of LDL receptor genetic variants
Supervisor: Mgr. Lukáš Tichý, 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.

Plant transposons and "genome landscape"
Supervisor: doc. RNDr. Eduard Kejnovský, CSc.

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.

Proteins interactions with DNA, focus on local DNA structures
Supervisor: prof. Mgr. Václav Brázda, Ph.D.

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.

Proteins involved in the regulation of telomeric repeats
Supervisor: doc. Mgr. Petra Procházková Schrumpfová, 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.

Proteomic insight into epigenetic regulation
Supervisor: Mgr. Gabriela Lochmanová, 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.

Qualitative and quantitative analysis of selected types of posttranslational modifications
Supervisor: prof. RNDr. Zbyněk Zdráhal, Dr.

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.

Structural Maintenance of Chromosomes (SMC) complexes
Supervisor: doc. Mgr. Jan Paleček, Dr. rer. nat.

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.

Structure-functional relationship of telomeres and telomerases
Supervisor: Mgr. Eva Sýkorová, 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.

Study of the effect of metformin and empagliflozin on the expression of enzymes of energy metabolism in an in vitro model of the proximal tubule
Supervisor: Mgr. Katarína Chalásová, Ph.D.

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.

Studying Adar null mice as a genetic model to understand the role of ADAR1 in innate immunity
Supervisor: prof. Mary Anne O'Connell, PhD.

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.

Subcellular trafficking in plant survival
Supervisor: Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Endosomal trafficking is vital in plant development both in optimal and stress conditions. This regulated vesicle trafficking is necessary for membrane integrity preservation and therefore plant resistance to acute osmotic stress. We identified proteins differentially localized along the secretory pathway in response to stress indicating their role in cellular stress response. Characterization of those proteins will provide insights into the role of subcellular machinery in plant response to stress and might have potential applications to engineer stress resistant plants that might be curial regarding incoming climate changes.
The PhD student will perform the physiological and cellular phenotype analysis of mutants and overexpression lines. The admitted candidate will perform genetic and molecular biology studies, including in situ protein localization and life confocal imaging techniques. In parallel the student will continue with the characterization of isolated candidate genes interactors.

Supervisor

Tomasz Nodzynski, B.A., M.Sc., Ph.D.

Telomere biology
Supervisor: prof. RNDr. Jiří Fajkus, CSc.

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.

The effect of homologous recombination on transcription
Supervisor: Mgr. Peter Kolesár, Ph.D.

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.

Tumor biology
Supervisor: doc. Mgr. Roman Hrstka, 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.

Co-translational quality control and its role in neural tissue
Supervisor: RNDr. Petr Těšina, Ph.D.

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

Requirements on candidates:

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

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

MORE INFORMATION:

http://ls-phd.ceitec.cz/

https://www.ceitec.eu/petr-tesina-research-group/rg396/tab?tabId=180

Notes

Recommended literature:

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

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

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

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

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

Supervisor

RNDr. Petr Těšina, Ph.D.

Designing modified DNA fragments
Supervisor: prof. RNDr. Radek Marek, Ph.D.

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

Requirements on candidates:

Computational and quantum chemistry, structural chemistry or biology.

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

MORE INFORMATION:

https://ls-phd.ceitec.cz/how-to-aplly/

https://www.ceitec.eu/structure-of-biosystems-and-molecular-materials/rg108

Notes

Recommended literature:

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

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

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

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

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

Supervisor

prof. RNDr. Radek Marek, Ph.D.

Dishevelled internal affairs in Wnt signalling
Supervisor: Konstantinos Tripsianes, 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

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor and phd@ceitec.muni.cz

MORE INFORMATION:

 

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.

Dynamic polymorphism of non-canonical nucleic acids in the intracellular space
Supervisor: doc. Mgr. Lukáš Trantírek, Ph.D.
i-Motifs (iMs) are four-stranded DNA structures that form at cytosine (C)-rich sequences in acidic conditions in vitro. Recent research utilizing the anti-iM antibody (iMab) (1) and in-cell NMR (2) has demonstrated the presence of iMs within the human genome and live cells. Additionally, in-cell NMR studies provided evidence that iMs formation is influenced by the cell cycle-dependent characteristics of the intracellular environment. This project aims to explore the connections between cell cycle-dependent iM formation, alterations in intracellular space properties, and the regulation of gene expression controlled by promoters containing iMforming sequences. Methodologically, the project integrates molecular biology and biophysical techniques with in-cell NMR spectroscopy.

Requirements on candidates:
Cell biology, DNA cloning, and/or NMR spectroscopy

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

MORE INFORMATION:

https://ls-phd.ceitec.cz/how-to-aplly/

https://www.ceitec.eu/non-coding-genome/rg109
Notes

Recommended literature:

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

Zanin et al. Genome-wide mapping of i-motifs reveals their association with transcription regulation in live human cells. Nucleic Acids Res. 2023 Sep 8;51(16):8309-8321.

Supervisor

doc. Mgr. Lukáš Trantírek, Ph.D.

Functions of cyclin-dependent kinase 11 (CDK11) in regulation of gene expression and tumorigenesis
Supervisor: Mgr. Dalibor Blažek, Ph.D.

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

Requirements on candidates:

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

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

MORE INFORMATION:

http://ls-phd.ceitec.cz/

https://www.ceitec.eu/inherited-diseases-transcriptional-regulation/rg38

Notes

Recommended literature:

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

Supervisor

Mgr. Dalibor Blažek, Ph.D.

Characterization of cyclin-dependent kinase 12 (CDK12) substrates and their roles in regulation of transcription and tumorigenesis
Supervisor: Mgr. Dalibor Blažek, Ph.D.

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

Requirements on candidates:

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

PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

MORE INFORMATION:

http://ls-phd.ceitec.cz/

https://www.ceitec.cz/dedicne-poruchy-transkripcni-regulace/rg38

Notes

Recommended literature:

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

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

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

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

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

Supervisor

Mgr. Dalibor Blažek, Ph.D.

Microenvironment models and their use to study agressivness and targeted therapy in B cell malignancies
Supervisor: prof. MUDr. Mgr. Marek Mráz, Ph.D.

Chronic lymphocytic leukemia (CLL) cells and indolent lymphomas are known to be dependent on diverse microenvironmental stimuli providing them signals for survival, development, proliferation, and therapy resistance. It is known that CLL cells undergo apoptosis after cultivation in vitro, and therefore it is necessary to use models of CLL microenvironment to culture CLL cells long-term and/or to study their proliferation. Several in vitro and in vivo models meet some of the characteristics of the natural microenvironment based on the 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 mechanisms leading to aggressiveness in B cell malignancies and/or novel therapeutic options, e.g. drugs targeting CLL proliferation, development of resistance in long-term culture or combinatory approaches, which cannot be analyzed in experiments based on the conventional culture of CLL/lymphoma primary cells. This project will utilize models developed in the laboratory and will further optimize and modify them. The biology of CLL and responses to targeted treatment will be interrogated using the developed models. The student will utilize various functional assays, Cripr editing, 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 that 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.
  • PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

    MORE INFORMATION:

    http://ls-phd.ceitec.cz/

    https://www.ceitec.eu/microenvironment-of-immune-cells/rg115

    Notes

    Recommended literature:

    Hoferkova E, Kadakova S, Mraz M. In Vitro and In Vivo Models of CLL-T Cell Interactions: Implications for Drug tetsing.Cancers (Basel). 2022 Jun 23;14(13):3087.

    Sharma et al. …Mraz. miR-29 Modulates CD40 Signaling in Chronic Lymphocytic Leukemia by Targeting TRAF4: an Axis Affected by BCR inhibitors. Blood 2021. https://pubmed.ncbi.nlm.nih.gov/33171493/

    Seda V. et al….Mraz. FoxO1-GAB1 Axis Regulates Homing Capacity and Tonic AKT Activity in Chronic Lymphocytic Leukemia. Blood, 2021, https://doi.org/10.1182/blood.2020008101.

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

    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.

    Peptide Sequence Motifs for Selective Targeting of Pathogens
    Supervisor: prof. RNDr. Robert Vácha, PhD.

    Antimicrobial peptides (AMPs) possess the ability to disrupt the membrane barrier function, effectively eliminating bacteria, viruses, and even cancer cells. Consequently, AMPs have emerged as promising candidates for the development of a new class of therapeutics. However, the majority of known AMPs exhibit toxic properties due to their origin from human-unfriendly sources, such as venoms. Our understanding of peptide targeting mechanisms towards specific pathogens and their membranes remains limited, hindering further peptide development. This ERC funded project aims to identify peptide sequence motifs that are responsible for selective targeting pathogens with respect to human cells. Apart from the differences in lipid composition of membranes, we will investigate the impact of membrane local curvature. The main tool for the study will be Molecular dynamics simulations with free energy calculations using Gromacs program package. These simulations will be complemented by in-house experiments providing crucial verification and feedback on peptide-membrane affinity. The acquired knowledge will guide the design of de novo peptides with enhanced pathogen-targeting specificity.

    Requirements on candidates:

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

    PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

    MORE INFORMATION:

    http://ls-phd.ceitec.cz/

    https://vacha.ceitec.cz/

    Notes

    Recommended literature:

    J Cell Biol. 2018; 217(9): 3109–3126, doi: 10.1083/jcb.201802027

    Colloids Surf B Biointerfaces 2017; 153:152-159, doi: 10.1016/j.colsurfb.2017.02.003

    Supervisor

    prof. RNDr. Robert Vácha, PhD.

    Regulation of protein liquid droplets during transcription
    Supervisor: prof. RNDr. Robert Vácha, PhD.

    Cells employ protein liquid droplets to form dynamic clusters, which function as nanoreactors or storages with the increased local concentration of specific protein components. These membrane-less organelles self-assemble based on weak protein-protein interactions of intrinsically disordered domains. However, the role of specific sequences remains elusive and the mixing between different protein droplets unexplored. This project is focused on the droplets involved in genome transcription, where posttranslational modifications control the droplet composition and regulate the transcription. Expected findings are not only important for the general knowledge but could also be useful in the design of new treatments because translocation malfunction is involved in numerous diseases including cancer. The research is strongly coupled to collaborations with excellent experimental teams and will be more closely discussed during the interview. The employed tools will contain multi-scale simulations using a wide range of advanced sampling techniques and development of protein parametrization.

    Requirements on candidates:

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

    PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

    MORE INFORMATION:

    https://ls-phd.ceitec.cz/how-to-aplly/

    https://vacha.ceitec.cz/

    Notes

    Recommended literature:

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

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

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

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

    Supervisor

    prof. RNDr. Robert Vácha, PhD.

    Structure of parallel forms of nucleic acids: NMR spectroscopy and molecular modelling
    Supervisor: prof. RNDr. Radek Marek, Ph.D.
    The project is focused on detailed structural characterization of short purine oligonucleotides clipped by proper sequential motifs that induce parallel orientation of DNA strands. For this purpose, NMR experiments combined with MD simulations will be employed. The effect of modifications of selected nucleotides on the structural properties of designed models will be investigated to gain deeper understanding of key interactions that contribute to the folding of such systems.

    Requirements on candidates:

    Structural chemistry or biology, advanced NMR spectroscopy, computational chemistry

    PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

    MORE INFORMATION:

    https://ls-phd.ceitec.cz/how-to-aplly/

    https://www.ceitec.eu/structure-of-biosystems-and-molecular-materials/rg108

    Notes

    Recommended literature:

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

    Supervisor

    prof. RNDr. Radek Marek, Ph.D.

    Translation in the context of human host-pathogen interaction
    Supervisor: RNDr. Petr Těšina, Ph.D.

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

    Requirements on candidates:

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

    PLEASE NOTE: before initiating the formal application process to doctoral studies, all interested candidates are required to contact the supervisor or/and fill in the registration form on the web page of the CEITEC PhD School (link below).

    MORE INFORMATION:

    http://ls-phd.ceitec.cz/

    https://www.ceitec.eu/petr-tesina-research-group/rg396/tab?tabId=180

    Notes

    Recommended literature:

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

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

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

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

    Supervisor

    RNDr. Petr Těšina, Ph.D.

    Supervisors

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