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SlovenčinaPhD programs
Biomedical Research Center of the Slovak Academy of Sciences participates on PhD study of 5 Faculties of 3 Slovak Universities, it is an external educational institution of the following Study programes:
| Faculty of Medicine Comenius University in Bratislava | Normal and Pathological Physiology |
| Oncology | |
| Faculty of Natural Sciences Comenius University in Bratislava | Molecular Biology |
| Genetics | |
| Microbiology and Virology | |
| Animal Physiology | |
| Biochemistry | |
| Faculty of Physical Education and Sport Comenius University in Bratislava | Sport Sciences |
| Faculty of Chemical and Food Technology Slovak University of Technology in Bratislava | Biochemistry |
| Faculty of Science Pavol Jozef Šafárik University in Košice | Zoology and Animal Physiology |
| Biophysics |
Theses for PhD study at the Biomedical Research Center of the Slovak Academy of Sciences for the academic year 2024/2025
Faculty of Science, Pavol Jozef Šafárik University in Košice
Deadline for application: 31. 5. 2024
More information on website of the faculty here.
| Study program: | Zoology and Animal Physiology |
| Form of study: | daily (full-time) |
| Thesis: | Activation of endogenous mechanisms leading to neuroprotection after stroke |
| Supervisor: | RNDr. Petra Bonová, PhD. |
| Email: | bonova@saske.sk |
| Keywords: | brain ischemia, ischemic tolerance, conditioning |
| Annotation: | Stroke represents a serious socio-economic problem with limited treatment options. Recently, the phenomenon of ischemic tolerance, i.e. endogenous stimulation of the mechanisms with the ability to induce neuroprotection, has become an attractive solution for the prevention and treatment of such conditions. Objectives: 1. Study of mechanisms of ischemic tolerance 2. Defining the role of peripheral blood cells in inducing ischemic tolerance 3. Testing of in vivo and ex vivo conditioning methods 4. Testing of conditioning methods in animal models of ischemic-reperfusion injury of nerve tissue |
| Study program: | Zoology and Animal Physiology |
| Form of study: | daily (full-time) |
| Thesis: | Mechanisms of endogenous repair following traumatic spinal cord injury |
| Supervisor: | MUDr. Karolína Kuchárová, PhD. |
| Email: | kkucharova@saske.sk |
| Keywords: | Traumatic spinal cord injury, Glial Scar, Neuroprotection, Neuroplasticity, Functional repair |
| Annotation: | Several experimental techniques that have led to improvements in neurological function after spinal cord injury (SCI) have not been translated into the clinic. Therefore, a better understanding of the molecular and cellular mechanisms that enhance functional regeneration following SCI may facilitate the translation of successful experimental findings into the clinic. The work will focus on the supporting cells that increase the Neuron/ Glia 2(NG2) proteoglycan expression after the SCI. When, where, and which NG2-expressing cell types respond to spinal cord injury and how these cells may be affected by local neuroregenerative successful (but invasive) approach will be compared with systemic cell-selective therapy. The response of NG2+ cell types to different treatments will be assessed by cell-specific and functional techniques. In the first aim, the project may uncover the mechanisms that block or promote the functional tissue repair after the SCI. In the second aim, the work may demonstrate whether a less invasive but cell-selective treatment can replace the experimentally successful local technique. |
| Study program: | Biophysics |
| Form of study: | daily (full-time) |
| Thesis: | Study of the effect of pathogenic mutations on the activity of the ryanodine receptor using allosteric models of channel gating |
| Supervisor: | Ing. Miloslav Karhánek, PhD. |
| Email: | miloslav.karhanek@savba.sk |
| Keywords: | mathematical modeling, Markov processes, ryanodine receptor, excitation-contraction coupling, genetic diseases |
| Annotation: | Ryanodine receptors (RyR) are ion channels responsible for control of excitation-contraction coupling in skeletal (RyR1) as well as cardiac muscle (RyR2). Pathogenic RyR mutations lead to dysregulation of channel activity by Ca2+ and Mg2+ ions, causing arrhythmias and malignant hyperthermia. The aim is to elucidate the effect of selected pathogenic mutations on the regulation of RyR activity by Ca2+ and Mg2+ ions, using allosteric models of channel gating. Methods: programming in C++; model optimization; Markov processes, reaction-diffusion equations |
| Study program: | Biophysics |
| Form of study: | daily (full-time) |
| Thesis: | Study of the effect of pathogenic mutations on the allosteric regulation of the ryanodine receptor using molecular simulation |
| Supervisor: | Ing. Miloslav Karhánek, PhD. |
| Email: | miloslav.karhanek@savba.sk |
| Keywords: | molecular simulation, ryanodine receptor, excitation-contraction coupling, genetic diseases |
| Annotation: | Ryanodine receptors (RyR) are ion channels responsible for control of excitation-contraction coupling in skeletal (RyR1) as well as cardiac muscle (RyR2). Pathogenic RyR mutations lead to dysregulation of channel activity by Ca2+ and Mg2+ ions, causing arrhythmias and malignant hyperthermia. The aim is to assess the effect of selected pathogenic mutations on the allosteric pathways between the binding sites of regulatory ligands (Ca2+, Mg2+, ATP, xanthines) and the gating mechanism in the RyR pore, using molecular simulation. Methods: structural biology; programs NAMD / GROMACS |
| Study program: | Biophysics |
| Form of study: | daily (full-time) |
| Thesis: | The use of modern methods of biophotonics for the study of the dynamics of the relationship of cellular structures in Wolfram syndrome |
| Supervisor: | RNDr. Michal Cagalinec, PhD. |
| Email: | michal.cagalinec@savba.sk |
| Keywords: | Confocal microscopy, mitochondria, metabolism, Wolfram Syndrome |
| Annotation: | The use of light in the investigation, diagnosis and therapy of diseases is growing rapidly underlined by unique properties of light radiation, the availability of high-performance light sources and detectors for its detection. In this regard, light microscopy represents an important area of application of these principles. In the work, we will use the up-to-date methods of confocal microscopy and super-resolution microscopy for the research of the structure and function of cells, their organelles and specific proteins to study rare disease Wolfram syndrome. |
| Study program: | Biophysics |
| Form of study: | daily (full-time) |
| Thesis: | Theoretical study of possible mechanisms of allosteric activation of calcium pump SERCA |
| Supervisor: | RNDr. Magdaléna Májeková, PhD. |
| Email: | magdalena.majekova@savba.sk |
| Keywords: | SERCA; allosteric activation; modulation function of ATP; molecular dynamics; HPC |
| Annotation: | Recent knowledge pointed out importance of disrupted calcium signaling in many pathological processes. A key role in the maintaining calcium homeostasis is ensured by calcium ATPase of sarco/endoplasmic reticulum SERCA, which pumps calcium ions from cytoplasm into lumen. The activity of SERCA, which can be decreased under pathological conditions, can be enhanced by activators. Their mechanism of action, so far unknown, could be based on the interference with the modulation effects of ATP. The main goal of the dissertation will be to contribute to a knowledge on modulation effects of ATP and mechanisms of allosteric activation of SERCA by means of molecular modeling and molecular dynamics methods. The work demands previous experience with the methods mentioned above as well as with high performance computing. |
Faculty of Natural Sciences, Comenius University in Bratislava
Deadline for application: 31. 05. 2024
More information on website of the faculty here.
| Study program: | Animal Physiology |
| Form of study: | daily (full-time) / externally |
| Thesis: | The role of inhibitory neurotransmission in neurodevelopmental diseases |
| Supervisor: | doc. RNDr. Ján Bakoš, PhD. |
| Email: | j.bakos@savba.sk |
| Keywords: | brain, GABA, development, autism |
| Annotation: | Gamma-aminobutyric acid (GABA) is one of the most important inhibitory neurotransmitters in the central nervous system. Increasing number of studies indicate that the formation of GABA-producing neurons, the differentiation of their subtypes, as well as the action of GABA on the postsynaptic membrane are important factors in brain development. The aim of the PhD project is to study markers and changes in inhibitory neurotransmission in brain areas relevant for the development of social behavior. The project includes use of transgenic mouse model of autism, immunostaining for postsynaptic proteins and behavioral evaluation for a comprehensive understanding of the mechanisms leading to neurodevelopmental diseases. |
| Study program: | Animal Physiology |
| Form of study: | daily (full-time) |
| Thesis: | Study of dynamics and morphology of cellular structures in experimental models of Wolfram syndrome |
| Supervisor: | RNDr. Michal Cagalinec, PhD. |
| Email: | michal.cagalinec@savba.sk |
| Keywords: | Wolfram Syndrome, confocal microscopy, transmission electron microscopy, mitochondria |
| Annotation: | Wolfram syndrome (WS) is a serious hereditary disorder originally classified as mitochondrial, but it was later shown that WS develops as a result of mutations in Wolframin 1 protein, located in the endoplasmic reticulum (ER) membrane. Why does a protein located in ER so strongly affect mitochondria? In the search for answers to these questions, we will use biochemical methods, molecular biology methods, immunofluorescence as well as electron microscopy. With the help of these methods, we determine the morphological and functional relationships of cell organelles and their proteins in experimental models of WS. |
| Study program: | Animal Physiology |
| Form of study: | daily (full-time) |
| Thesis: | The impact of myositis and exercise on metabolism and secretory activity of skeletal muscle: in vitro studies on the model of human muscle cells |
| Supervisor: | prof. MUDr. Barbara Ukropcová, PhD. |
| Email: | barbara.ukropcova@savba.sk |
| Keywords: | idiopathic inflammatory myopathies, exercise, skeletal muscle, human muscle cells, electric pulse stimulation, metabolism, myokines |
| Annotation: | Idiopathic inflammatory myopathies (IIM) are heterogenous group of disorders that affect muscle functional capacity. Skeletal muscle metabolic dysfunction contributes to the pathogenesis of IIM, and can be favourable affected by regular exercise. Our aim is to study metabolism and secretory function of human primary muscle cells, derived from patients with IIM before and after 6-month intervention (exercise or pharmacotherapy). Electric pulse stimulation, the model of exercise in vitro, will be used to assess the direct effects of exercise on the release of myokines from contracting muscle cells. |
| Study program: | Animal Physiology |
| Form of study: | daily (full-time) |
| Thesis: | Extracellular vesicles as modulators of systemic and tissue-specific metabolic flexibility: the impact of exercise and complex lifestyle modification in patients with obesity |
| Supervisor: | Mgr. Jozef Ukropec, DrSc. |
| Email: | jozef.ukropec@savba.sk |
| Keywords: | metabolic flexibility, obesity, lifestyle intervention, exercise, extracellular vesicles |
| Annotation: | Obesity is the leading risk factor of a spectrum of chronic diseases, highly prevalent in Slovak population. Metabolic flexibility is an important determinant of the whole-body metabolic health with the capacity to modulate effectiveness of the response to exercise & lifestyle interventions. Lifestyle modification is a cornerstone of obesity management, and aim of this work is to characterize the clinical parameters and molecular biomarkers of metabolic flexibility contained in exosomes released in energetically challenging situations. Ultimately, we would like to define and validate a biomarker predicting the response to a lifestyle intervention, which would allow presonalised precission medicine for obesity and obesity associated chronic diseases, including metabolic and neurodegenerative diseases. |
| Study program: | Genetics |
| Form of study: | daily (full-time) |
| Thesis: | DNA methylation as prognostic biomarker in pancreatic ductal adenocarcinoma |
| Supervisor: | Mgr. Božena Smolková, PhD. |
| Email: | bozena.smolkova@savba.sk |
| Keywords: | pancreatic ductal adenocarcinoma, liquid biopsy, prognostic marker, predictive marker, preclinical model |
| Annotation: | Introducing novel techniques for detecting tumor-specific DNA methylation in the plasma of patients with pancreatic ductal adenocarcinoma (PDAC). Identifying prognostic and predictive molecular markers and validating their correlation between tumors and plasma. Exploring therapeutic targeting of selected markers using specific inhibitors in preclinical models of PDAC. |
| Study program: | Molecular Biology |
| Form of study: | daily (full-time) |
| Thesis: | Relationship between mitochondrial insufficiency and the regulation of the expression of proteins of EC coupling |
| Supervisor: | RNDr. Alexandra Zahradníková ml., PhD. |
| Email: | saschia.zahradnikova@savba.sk |
| Keywords: | mitochondrial disease, cardiac myocytes, expression regulation |
| Annotation: | Mitochondrial insufficiency are linked with cardiac pathologies, which are the result of dysregulation of different structural and functional proteins. The aim of the thesis will be to clarify the molecular-biological processes involved in the regulation of selected cardiospecific proteins and elucidate their role in mitochondrial diseases leading to heart failure. |
| Study program: | Molecular Biology |
| Form of study: | daily (full-time) |
| Thesis: | Study of tick-borne encephalitis virus – host interactions in the skin ex vivo |
| Supervisor: | Mgr. Pavlína Bartíková, PhD. |
| Email: | pavlina.bartikova@savba.sk |
| Keywords: | Tick-borne encephalitis virus, skin, innate immune response, cytokines |
| Annotation: | It is generally known that tick-borne encephalitis virus is neurotropic and the most common way to get infection is through biting of infected ticks. Thus, the outcome of the infection is influenced by the interactive events between ticks, virus and the host in the skin. However, information about them is very scarce. Using human skin ex vivo model can help to understand and elucidate some of the molecular mechanisms of infection in the skin and fill in some missing puzzle pieces to the knowledge of the complexity of virus – host. Aims of thesis: to establish cultivation of human skin explants in our laboratories; to set up appropriate infection; observation, exploration and comparative analysis of mutual interactions – replication and spread of virus versus innate immune response in skin explants after infection |
| Study program: | Molecular Biology |
| Form of study: | daily (full-time) |
| Thesis: | The impact of myositis and exercise on metabolism and secretory activity of skeletal muscle: in vitro studies on the model of human muscle cells |
| Supervisor: | Mgr. Jozef Ukropec, DrSc. |
| Email: | jozef.ukropec@savba.sk |
| Keywords: | idiopathic inflammatory myopathies, exercise, skeletal muscle, human muscle cells, electric pulse stimulation, metabolism, myokines |
| Annotation: | Idiopathic inflammatory myopathies (IIM) are heterogenous group of disorders that affect muscle functional capacity. Skeletal muscle metabolic dysfunction contributes to the pathogenesis of IIM, and can be favourable affected by regular exercise. Our aim is to study metabolism and secretory function of human primary muscle cells, derived from patients with IIM before and after 6-month intervention (exercise or pharmacotherapy). Electric pulse stimulation, the model of exercise in vitro, will be used to assess the direct effects of exercise on the release of myokines from contracting muscle cells. |
| Study program: | Molecular Biology |
| Form of study: | daily (full-time) |
| Thesis: | Extracellular vesicles as modulators of systemic and tissue-specific metabolic flexibility: the impact of exercise and complex lifestyle modification in patients with obesity |
| Supervisor: | Mgr. Jozef Ukropec, DrSc. |
| Email: | jozef.ukropec@savba.sk |
| Keywords: | metabolic flexibility, obesity, lifestyle intervention, exercise, extracellular vesicles |
| Annotation: | Obesity is the leading risk factor of a spectrum of chronic diseases, highly prevalent in Slovak population. Metabolic flexibility is an important determinant of the whole-body metabolic health with the capacity to modulate effectiveness of the response to exercise & lifestyle interventions. Lifestyle modification is a cornerstone of obesity management, and aim of this work is to characterize the clinical parameters and molecular biomarkers of metabolic flexibility contained in exosomes released in energetically challenging situations. Ultimately, we would like to define and validate a biomarker predicting the response to a lifestyle intervention, which would allow presonalised precission medicine for obesity and obesity associated chronic diseases, including metabolic and neurodegenerative diseases. |
| Study program: | Microbiology and Virology |
| Form of study: | daily (full-time) |
| Thesis: | Study of tick-borne encephalitis virus – host interactions in the skin ex vivo |
| Supervisor: | Mgr. Pavlína Bartíková, PhD. |
| Email: | pavlina.bartikova@savba.sk |
| Keywords: | Tick-borne encephalitis virus, skin, innate immune response, cytokines |
| Annotation: | It is generally known that tick-borne encephalitis virus is neurotropic and the most common way to get infection is through biting of infected ticks. Thus, the outcome of the infection is influenced by the interactive events between ticks, virus and the host in the skin. However, information about them is very scarce. Using human skin ex vivo model can help to understand and elucidate some of the molecular mechanisms of infection in the skin and fill in some missing puzzle pieces to the knowledge of the complexity of virus – host. Aims of thesis: to establish cultivation of human skin explants in our laboratories; to set up appropriate infection; observation, exploration and comparative analysis of mutual interactions – replication and spread of virus versus innate immune response in skin explants after infection |
| Study program: | Biochemistry |
| Form of study: | daily (full-time) |
| Thesis: | Extracellular vesicles as modulators of systemic and tissue-specific metabolic flexibility: the impact of exercise and complex lifestyle modification in patients with obesity |
| Supervisor: | Mgr. Jozef Ukropec, DrSc. |
| Email: | jozef.ukropec@savba.sk |
| Keywords: | metabolic flexibility, obesity, lifestyle intervention, exercise, extracellular vesicles |
| Annotation: | Obesity is the leading risk factor of a spectrum of chronic diseases, highly prevalent in Slovak population. Metabolic flexibility is an important determinant of the whole-body metabolic health with the capacity to modulate effectiveness of the response to exercise & lifestyle interventions. Lifestyle modification is a cornerstone of obesity management, and aim of this work is to characterize the clinical parameters and molecular biomarkers of metabolic flexibility contained in exosomes released in energetically challenging situations. Ultimately, we would like to define and validate a biomarker predicting the response to a lifestyle intervention, which would allow presonalised precission medicine for obesity and obesity associated chronic diseases, including metabolic and neurodegenerative diseases. |
Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava
Deadline for application: 31. 05. 2024
More information on website of the faculty here.
| Study program: | Biochemistry |
| Form of study: | daily (full-time) |
| Thesis: | Molecular fingerprint of host-uropathogen co-metabolism: a key to early diagnostics of urinary tract infections |
| Supervisor: | Ing. Ľudovít Škultéty, DrSc. |
| Email: | ludovit.skultety@savba.sk |
| Keywords: | uropathogens, urinary tract infections, molecular profile |
| Annotation: | Bacterial uropathogens’ secretion of virulence factors and attenuation of host immune system are leading cause of the development of urinary tract infections (UTIs) that affect 150 million people of all ages annually worldwide. The timely and accurate identification of uropathogens is central to managing UTIs. However, common diagnostics like presence of clinical symptoms and urine culturing could be unspecific and time-consuming. First, in in vitro bacteria-renal cells model, we will define a species-specific metabolomics profile reflecting mutual molecular interactions between the uropathogen and the host. Second, we will correlate and quantify the distribution of uropathogen siderophores and quorum sensing molecules with pathological metabolism alterations of lipids, amino acids, tricarboxylic acid cycle, and distribution of antimicrobial peptides of the urinary tract at the regional and subregional level. Third, we will develop a diagnostic tool for early detection of UTIs and co-infections based on the proposed host-metabolic signature in urine. The interdisciplinary thesis aims to develop an original early diagnostics platform for urinary tract infection diseases based on specific host-uropathogenic interaction and its unique molecular profile. |
| Study program: | Biochemistry |
| Form of study: | daily (full-time) |
| Thesis: | Spatial metabolomics in central nervous system infections |
| Supervisor: | Ing. Ľudovít Škultéty, DrSc. |
| Email: | ludovit.skultety@savba.sk |
| Keywords: | Spatial metabolomics, Central nervous system infections |
| Annotation: | Bacterial, fungal, and viral pathogens penetrating the nervous system of patients at risk (including neonates) trigger an immune cascade resulting in inflammation, leading to altered metabolic pathways and neuropathological changes in the brain. Blood and cerebrospinal fluid culture, serology, and PCR analysis are invasive with limited sensitivity and specificity. First, in the rat model, we will define the molecular mechanisms by which the pathogens interact with and penetrate the blood-brain and brain-cerebrospinal fluid barriers and correlate microbial invasion with pathological brain metabolism alterations at the regional and subregional levels. Second, we will quantify and correlate host neurotransmitters, neuropeptides, and brain lipids with pathogen-specific virulence metabolic biomarkers by spatial-metabolomics during CNS infection progression. Third, we will develop a noninvasive diagnostic tool for early detection of CNS infections and superinfections based on the proposed host-pathogen metabolic signature in urine and serum specimens and nasal swabs. The interdisciplinary thesis aims to reduce the mortality and morbidity of patients with CNS infections by developing an original early diagnostics platform based on specific infection-related metabolic biomarkers. |
