Animal physiology, immunology and developmental biology

Doctoral degree in full-time or combined form. The language of instruction is Czech.

The programme can be studied only as a single subject.

Application deadline depending on the admission procedure chosen (midnight 30 November 2022 or 15 December 2022)

What will you learn?

The aim of the program is to prepare top specialists in specific scientific fields developed within the Department of Animal Physiology and Immunology at the Institute of Experimental Biology, Faculty of Science, Masaryk University. Graduates are prepared for further scientific careers at workplaces of basic or applied research at the international level, but also for possible employment in companies with a research background, in medical facilities and as professional lecturers.

The program focuses on the research formation of students in the rapidly developing fields of physiology, immunology and developmental biology. Students are trained to conduct research in the areas ranging from cellular to organ level to models of whole animal organisms from cells to humans. Modern molecular biology techniques and state-of-the-art imaging techniques are applied. The program covers research topics ranging from veterinary through biomedical applications to general basic research issues. In particular, the most represented topic is the research of cellular signaling, which is crucial for understanding the processes controlling embryonic development, tissue differentiation and regeneration, as well as processes of carcinogenesis or immune regulation. The program integrates methodological approaches of molecular biology, molecular embryology and cell biology with morphological and behavioral approaches.

The course is designed to motivate prospective students through checkpoints. A greater number of methodologically oriented courses, internships, and openness to contacts with biotechnology companies ensure interconnection with the practice of modern biological research. Emphasis is placed on using English as a basic tool for scientific work.

Students are motivated by the high professional quality of research in an open and friendly environment. The performance of individual students is appreciated both financially and, for example, through participation in prestigious international conferences.

Practical training

The program includes compulsory student practice at potential employers as a tool for establishing links with future employers.

Career opportunities

The program is designed to be comparable with high-quality foreign universities programmes and graduates work well at top research institutes, whether from academic or non-academic institutions. The director of the Academy of Sciences of the Czech Republic, Key Manager of Roche Diagnostics, Postdoc at the Karolinska Institutet or the director of the embryological laboratory are examples of positions where our graduates found employment and refer for the program. Graduates of the doctoral study program are therefore entitled to carry out independent scientific and research activities in the field of basic and applied research, but they are also employed in management positions thanks to their language and managerial competencies. In a broader sense, they are prepared to carry out all activities related to scientific work; to deal with conceptual issues, scientific-organizational activities and teaching.

Admission requirements

Admission procedure
Admission board checks the candidates' professional capacities in an entrance interview that is conducted in English. The candidates submit a structured CV and in the course of the interview, they will present a brief proposal of their PhD project, will define the anticipated outputs, and suggest a methodical procedure. Written plan of candidate's suggested research project is also mandatory and will be submitted to the board. Recommended length of the plan is two pages and the structure is as follows: Title, Name of applicant, Name of supervisor, Home institution, Synopsis, Aims, Methodology, Financial covering. In a discussion with the admission board and in the presence of their supervisor they have to demonstrate that their respective thesis topic is scientifically well-grounded and experimentally manageable. A necessary prerequisite for admission is a demonstrable capability of professional conversation in English. The sufficient financial coverage of the candidate's scientific project will be assessed by the admission board within the terms of the entrance interview and further within the terms of the PhD Workshop in the 3rd semester.
The admission board assesses the candidates’ knowledge and prerequisites for the independent scientific work (0-200 points) and the capability of communication in English (0-100 points).

More information about admission process for international applicants in general can be found here.

Date of the entrance exam
The applicants will receive information about the entrance exam by e-mail usually at least 10 days before the exam.
Please, always check your e-mails, including spam folders.

Conditions of admission
To be admitted, the candidate must obtain at least 120 points in the professional and at least 60 points in the language part of the interview.
Successful applicants are informed of their acceptance by e-mail and subsequently receive an invitation to the enrolment.

Programme capacity
The capacity of a given programme is not fixed; students are admitted based on a decision by the Doctoral Board after assessing their aptitude for study and motivation.


2 May – 15 Dec 2022

Submit your application during this period

International applicants for doctoral study (Czech and Slovak Republics applicants not included)

1 Aug – 30 Nov 2022

Submit your application during this period

Admission to Doctoral degree programmes in 2022/2023 (beginning: Spring 2023)

Dissertation topics

Single-subject studies

Atypical human kinase Haspin – its biological interactions and role in cell plasticity
Supervisor: Mgr. Karel Souček, Ph.D.

Inhibition of cell-cycle regulators, such as cyclin-dependent kinases and checkpoint kinases, recently emerged as attractive strategy for the treatment of multiple types of cancer. Haspin is an atypical serine/threonine kinase with well described role in normal mitosis, but significantly understudied role in the interphase of the cell cycle and its regulation. PhD candidate will use our new recently discovered exquisitely selective Haspin inhibitors and investigate function of the kinase
in cell cycle regulation and the therapeutic potential of its pharmacological inhibition. Specifically, he/she will thoroughly characterize effects of Haspin inhibition on the cell cycle progression using single cell tracking; and analyze the Haspin interactome (using BioID) to discover its changes during interphase and mitosis. Since the role of Haspin in cancer cell
dissemination is completely unknown, he/she will also investigate it in the context of cancer cell plasticity. This research will unravel in detail the role of Haspin in cell cycle and clarify the function of this attractive therapeutic target.


Mgr. Karel Souček, Ph.D.

Dynamics of cancer cell surface fingerprint plasticity in epithelial-to-mesenchymal transition
Supervisor: Mgr. Karel Souček, Ph.D.

The epithelial-mesenchymal plasticity, in tight association with stemness, contributes to the homeostasis, evolution of early neoplastic lesions, and cancer dissemination. The ability of tumor cells to adapt to such dynamic changes in the microenvironment is considered a key requirement for their survival and outgrowth. The process which most likely interlinks the cancer cell plasticity with their dissemination capability, and adaptation to microenvironmental factors is the epithelial-to-mesenchymal transition (EMT). In this project you will tackle the molecular basis of regulation of cell surface fingerprint associating with EMT in the context of cancer cell plasticity, tumor dissemination, and tumor & metastatic microenvironment. We expect that this research will unravel in detail the regulation of EMT surfaceome as a critical element in the multi-step process of tumor dissemination and clarify the function of this attractive therapeutic target for solid tumors.


Mgr. Karel Souček, Ph.D.

Molecular and cellular processes deregulated during the developmental neurotoxicity induced by xenobiotics
Supervisor: RNDr. Miroslav Machala, CSc.

Vývojová neurotoxicita (z angl. developmental neurotoxicity) představuje až do nedávna velmi podceňovanou oblast toxikologie. Až nedávné studie prokazující spojitost mezi chronickou expozicí savců látkám znečišťujícím trvale naše životní prostředí (např. zpomalovače hoření či pesticidy a jiné polutanty) a zvýšenou incidencí neurologických poruch typu roztroušená skleróza, parkinsonismus či autismus poukázali na zásadní nedostatek buněčných modelů, které by umožnili rutinní testování xenobiotik a polutantů s ohledem na jejich DNT potenciál. Tématem této práce je proto zavedení metodologického panelu, který umožní stanovení relativních efektivních potenciálů (REP) vybraných suspektních neurotoxikantů a následné objasnění buněčných a molekulárních procesů, které stojí za jejich neurotoxicitou.


RNDr. Miroslav Machala, CSc.

Pathogens modulation of immune parameters on honey bees
Supervisor: doc. RNDr. Pavel Hyršl, Ph.D.

1. rok: V rámci programu Erasmus+ uskutečnit studijní pobyt na některé z partnerských univerzit. Začátek experimentů – odběry a zpracování vzorků. 2. rok: Zpracovat vzorky odebrané během řešení grantového projektu, vyzkoušet a optimalizovat různé metody stanovení imunitních parametrů u hmyzu. Prezentace první části výsledků. 3. rok: Zpracovat další vzorky, porovnání výsledků mezi několika modelovými organismy. Příprava manuskriptu pro publikaci. 4. rok: Celková prezentace výsledků. Předpokládá se spolupráce na dalších publikacích.


doc. RNDr. Pavel Hyršl, Ph.D.

Pathophysiology of Sprouty proteins and their association with ciliopathies
Supervisor: doc. RNDr. Marcela Buchtová, Ph.D.

Sprouty proteiny představují kontrolní mechanismus signalingu aktivovaných tyrosinkinázových receptorů, včetně FGF signální dráhy. U myší způsobuje delece Sprouty vývojové poruchy vedoucí k poškození sluchu, kraniofaciálním defektům, zpomalenému postnatálnímu růstu nebo jícnové achalázii a střevní pseudoobstrukci. Význam lidského genu Sprouty2 byl zaznamenán u nefropatie, thanatoforické dysplázie a v různých typech onkologických onemocnění. V poslední době se ukazuje, že syndromy podmíněné hyperaktivací signální dráhy růstových fibroblastových faktorů (FGF) a syndromy spojené s deregulovanou funkcí primárních cilií se projevují řadou společných fenotypů, kromě jiných také u kraniofaciálních a achondroplastických malformací. PhD projekt se zaměří na charakterizaci role Sprouty proteinů v průběhu skeletogeneze, vyhodnotíme vývojové defekty tkání a orgánů myšího modelu s deletovaným Sprouty2 a Sprouty 4, které se běžně vyskytují u ciliopatií a zanalyzujeme signální dráhy modulované primárními ciliemi v morfogenezi Sprouty deficientních myší.


doc. RNDr. Marcela Buchtová, Ph.D.

Prognostic and predictive markers of squamous cell carcinoma invasion in the oral cavity and oropharynx
Supervisor: doc. RNDr. Marcela Buchtová, Ph.D.

Karcinomy dutiny ústní a orofaryngu patří mezi deset nejčastěji se vyskytujících malignit v lidské populaci. Náš projekt je zaměřen na spinocelulární karcinom, který představuje v této oblasti nejfrekventovanější typ maligního onemocnění. Prognóza onemocnění zhoubným nádorem dutiny ústní a orofaryngu je dána především stupněm invazivity primárního tumoru a rozsahem metastatického postižení regionálních a vzdálených uzlin. Intenzita perineurální invaze koreluje s lokalizací nádoru, jeho rozsahem a přítomností uzlinových metastáz. PhD projekt bude zaměřen na determinaci klinicky relevantních somatických mutací u pacientů s perineurální invazí a na analýzu exprese raných molekulárních markerů perineurální invaze na rozhraní nádorové a okolní tkáně. Dále se zaměří na analýzu úlohy primárních cilií a Sonic Hedgehog dráhy v buňkách spinocelulárního karcinomu a vliv modifikované SHH signalizace na jejich perineurální invazi.


doc. RNDr. Marcela Buchtová, Ph.D.

Regulation of cardiomyocytogenesis in pluripotent stem cells
Supervisor: Mgr. Jiří Pacherník, Ph.D.

Cílem je studovat mechanismy kardiomyocytogeneze u pluripotentních kmenových buněk in vitro. Metody: literární rešerše, metody tkáňových kultur, metody molekulární biologie, atd... Studia zaměřená na regulaci četnosti vznikajících kardiomyocytů, jejich specifikaci a maturaci. Modely: lidské indukované pluripotentní buňky z pacientů i zdravých dárců, linie myších embryonálních kmenových buněk, tkáňové řezy, a další.


Mgr. Jiří Pacherník, Ph.D.

Role of LGR5-positive stem cells in odontogenesis
Supervisor: doc. RNDr. Marcela Buchtová, Ph.D.

Náhradní zubní generace se u obratlovců vyvíjejí ze zubní lišty. Doba trvání a morfologie zubní lišty se mezidruhově liší v závislosti na tom kolik generací zubů je iniciováno během života jedince. PhD projekt se zaměří na analýzu lokalizace LGR5-pozitivních progenitorových buněk během odontogeneze a jejich osudu. Dále bude sledovat expresní profil LGR5-pozitivních buněk a signalizaci kontrolující formování zubní lišty. S využitím experimentálních přístupů zaměřených na zvýšení či snížení WNT signalizace bude provedena analýza úlohy této dráhy v iniciaci náhradní zubní lišty. Tato studie regulace zachování progenitorových buněk v zubní liště povede k odhalení procesů, které jsou podkladem druhově specifického potenciálu formování daného počtu generací zubů, jakož i patologických stavů u člověka, kde je tvorba náhradní dentice narušena.


doc. RNDr. Marcela Buchtová, Ph.D.

The impacts of magnetic fields on animal biological clock.
Supervisor: doc. RNDr. Martin Vácha, Ph.D.

Zjistili jsme, že vnitřní hodiny hmyzu jsou ovlivnitelné slabými magnetickými a elektromagnetickými poli, která se vyskytují zejména v blízkosti technických zařízení. Správný cirkadiánní rytmus je přitom v pozadí mnoha funkcí organismu a jeho poruchy vedou k řadě chorob. Projekt se bude věnovat zcela novému oboru studia kombinujícímu výzkum cirkadiánní rytmicity zvířat s výzkumem citlivosti biologických systémů na slabá magnetická pole. Pole těchto parametrů obklopují technická zařízení a mohou mít environmentální i zdravotní dopady. Experimentální část práce bude postavena na technikách behaviorálních a molekulárně biologických. Na hmyzích a savčích modelech má ukázat, jaká je citlivost tohoto jevu a jaký je jeho mechanismus a podstata.


doc. RNDr. Martin Vácha, Ph.D.

The mechanisms of chemically induced tumor progression in lung and bronchial cellular models - the role of exosomes
Supervisor: RNDr. Miroslav Machala, CSc.

Polycyclic aromatic hydrocarbons (PAHs) such as benzo/a/pyrene (BaP) and persistent dioxin-like compounds (DLCs) such as 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) belong among the most important airborne and foodborne environmental toxicants, and the lungs represent one of their major target organs. However, in spite of many in vivo and in vitro studies, the mechanisms of toxicity and carcinogenicity of PAHs and DLCs in respiratory system are insufficiently characterized. Chronic exposure to PAHs contributes to genotoxicity and to the development of (non-genotoxic) “dioxin-like“ toxicity via activation of aryl hydrocarbon receptor (AhR), including promotion/progression of lung cancer. Chemically-induced carcinogenesis involves numerous strategies recruited by transformed cells, which allow them to survive and to obtain adaptive advantages over the normal cells. A comprehensive evaluation of changes in gene expression, cell population parameters (such as cell cycle and proliferation), formation and release of extracellular vesicles will allow us to compare impact of PAHs and DLCs on normal and transformed airway cells and to identify novel suitable biomarkers of dioxin-like toxicity and/or AhR-dependent genotoxicity.

  • investigation of changes in gene expression, phenotype and function of HBEC models during their transformation induced by TCDD, BaP or other PAHs or complex extract of airborne particles and estimation of relative effective potencies in selected in vitro models/parameters;
  • characterization of extracellular vesicles produced by normal and chemically transformed cells.

cell growth and maintenance, cytokinetic parameters, migration/invasion assays, cell morphology visualisation, detection of EMT- and cell transformation-related gene expression and protein expression (cell culturing, flow cytometry, fluorescent microscopy, Western blotting, qRT-PCR, ultracentrifugation and other molecular biological, biochemical and cytological methods).
Experimental work will be performed at the Veterinary Research Institute, Brno


RNDr. Miroslav Machala, CSc.

The metabolism of glycosphingolipids and its potential roles in colon cancer cells
Supervisor: prof. RNDr. Jan Vondráček, Ph.D.

Nádory tlustého střeva představují častý a závažný typ nádorového onemocnění v jehož průběhu dochází k reprogramování složení a metabolismu buněčných lipidů. Cílem práce je, s využitím kombinace in vivo dat a vhodných in vitro modelů, definovat funkční úlohu vybraných drah metabolismu glykosfingolipidů v modulaci vlastností nádorových buněk tlustého střeva, a získat vhodné nástroje pro studium metabolismu glykosfingolipidů v primárních vzorcích odebraných pacientům ve spolupráci s klinickými pracovišti. Výsledky mohou mít potenciální využití v diagnostice a terapii tohoto onemocnění.


prof. RNDr. Jan Vondráček, Ph.D.

The trade-offs in longevity and immunity in worker honey bees, Apis mellifera
Supervisor: Mgr. Pavel Dobeš, Ph.D.

This project aims to acquire information about redox homeostasis in honey bees with emphasis on how it is affected by Varroa destructor and other bee pathogens infection, how it differs seasonally, and how it is modified in long-living winter bees. Antioxidant system components, both enzymatic and non-enzymatic, as well as hemocytes and other immune system components participating in response to pathogens and maintenance of homeostasis, will be thoroughly examined using a complex methodological approach that will also allow the assessment of reactive oxygen and nitrogen species production, among other parameters.


Mgr. Pavel Dobeš, Ph.D.

Xenotransplants of metastatic carcinoma as a tool for preclinical research
Supervisor: Mgr. Karel Souček, Ph.D.

Despite the recent advent of targeted antitumor therapies, metastatic disease
remains incurable and accounts for the vast majority of cancer-related
deaths. The lack of relevant models, reproducing the pathophysiology of
human metastasis limits the progress in the therapy of this bleak
complication of cancer. These models are needed for understanding of the
complexity of cancer biology in the late disease stage and also for testing of
new treatment options. The sampling of metastatic tumors is rare and
mostly not feasible. Therefore, circulating tumor cells (CTCs), isolated from
peripheral blood represent a promising source of material for relevant
preclinical analyses. Given the relatively low number of CTCs, orthotopic
implantation or sub-renal capsule transplantation of CTCs into the
immunodeficient animals represents an option for amplification of this
limited resource. Such permanent CTC-derived xenografts (CDX) may fully
recapitulate the plasticity and heterogeneity of cancer, and thus enable
advanced in vivo drug screens as well as comprehensive genomic, transcriptomic and proteomic profiling.

The aim of this project is: 1) To establish a biobank of CDXs from
metastatic breast (BCa), prostate (PCa) and pancreatic (PanCa) cancer
patients. CTCs from peripheral blood of consented patients will be depleted
for CD45+ leukocytes and the remaining CD45- fraction will be implanted
under the renal capsule (PCa&PanCa CTCs) or into the mammary fat pad
(BCa CTCs) of immunodeficient animals. Obtained tumors will be
characterized, propagated, annotated and biobanked. 2) To perform
genomic and transcriptomic profiling of obtained models, and to
characterize their inter- and intra-tumoral heterogeneity. 3) To perform
preclinical in vivo study. Altogether, we propose the establishment of CTCderived
xenografts, characterized both on cellular and molecular level that
can be exploited for personalized therapy selection for patients with
metastatic disease. 4) To introduce optimized methodology for isolation,
handling and characterization of CTCs in the laboratory of clinical partners
(MMCI, UHOL) and propose it to other health-care facilities in the Czech


Mgr. Karel Souček, Ph.D.

Study information

Provided by Faculty of Science
Type of studies Doctoral
Mode full-time Yes
combined Yes
distance No
Study options single-subject studies Yes
single-subject studies with specialization No
major/minor studies No
Standard length of studies 4 years
Language of instruction Czech
Collaborating institutions
  • The Czech Academy of Sciences
  • Biofyzikální ústav AV ČR
  • Ústav biologie obratlovců AV ČR
Doctoral board and doctoral committees

Do you have any questions?
Send us an e-mail to

prof. Mgr. Vítězslav Bryja, Ph.D.



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