PhD programs

PhD programs

Biomedical Research Center of the Slovak Academy of Sciences participates on PhD study of 5 Faculties of 4 Slovak Universities, it is an external educational institution of the following study programmes:

Faculty of Medicine
Comenius University in Bratislava
7.1.3 Normal and Pathological Physiology
7.1.15 Oncology
Faculty of Natural Sciences
Comenius University in Bratislava
4.2.3 Molecular Biology
4.2.4 Genetics
4.2.7 Microbiology
4.2.10 Animal Physiology
4.2.13 Virology
Faculty of Chemical and Food Technology
Slovak University of Technology in Bratislava
4.1.22 Biochemistry
Faculty of Science
Pavol Jozef Šafárik University in Košice
4.2.10. Physiology of Animals
University of Veterinary Medicine and Pharmacy in Košice4.2.7 Microbiology
4.2.13 Virology

Theses for PhD study at the Biomedical Research Center of the Slovak Academy of Sciences for the academic year 2020/2021

 

Faculty of Natural Sciences, Comenius University in Bratislava

 

Deadline for application: 31. 05. 2020

More information on website of the faculty here.

Study programm: Animal Physiology
Form of study: daily (full-time) or external
Thesis: Molecular physiology of the effects elicited by aerobic-strength training in cancer survivors
Supervisor: Mgr. Jozef Ukropec, DrSc.
Email: Jozef.ukropec@savba.sk
Keywords: Testicular germ cell carcinoma, regular exercise, chemotherapy related late toxicity, skeletal muscle, metabolism, primary muscle cell culture, insulin sensitivity
Annotation: Regular exercise is effective in prevention & treatment of chronic diseases. Presence of chronic metabolic disease is in cancer survivors commonly associated with the chemotherapy-related late toxicity, and could be significantly lowered by exercise-induced improvements in physical fitness. We will study mechanisms synchronizing adaptive response to regular exercise involving muscle derived bioactive molecules. We hypothesize that they are not only involved in improvements of muscle integrity and functional capacity but also have profound metabolicallz relevant systemic effects. Muscle satellite cells derived culture will be used as a model to test our hypotheses and the data will be interpreted in light of the results from the exercise intervention study in cancer survivors.

Study programm: Animal Physiology
Form of study: daily (full-time) or external
Thesis: The role of skeletal muscle in systemic addaptive response to regular exercise in humans: epigenetic mechanisms and molecular mediators
Supervisor: Doc. MUDr. Barbara Ukropcová, PhD .
Email: barbara.ukropcova@savba.sk
Keywords: regular exercise, healthy ageing, skeletal muscle, metabolism, primary muscle cell culture, epigenetic adaptation
Annotation: Regular exercise is effective in prevention & treatment of chronic diseases and it supports healthy ageing. We focus on the integrated adaptive response to exercise, potentially mediated by molecules released from contracting muscle as well as from other tissues during exercise. We assume that these molecules can modulate structure and function of other organs, including brain. Mechanisms of exercise-induced adaptive response will be studied in circulation, cerebrospinal fluid and in skeletal muscle in vivo (MR spectroscopy), ex vivo (biopsy) and in vitro, in primary human muscle cells. The data will be interpreted in relationship with metabolism, fitness, cognitive functions and brain volumetry (MRI) as well as their changes, induced by acute and regular exercise.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Metabolis therapy of the heart failure: impact to metabolism and morphology of cardiac myocytes
Supervisor: RNDr. Michal Cagalinec, PhD.
Email: Michal.cagalinec@savba.sk
Keywords: Heart failure, metabolic therapy, cardiac myocytes, ultrastructure, calcium metabolism, contractility
Annotation: Heart failure (HF) is a major cause of death worldwide, associated with perturbations of energy metabolism, morphological and functional adaptations. Here, the therapy with two B vitamins can protect against these negative adaptations in HF with respect of mitochondrial metabolism. However, it is not clear, how effective is this therapy in case of functional and morphological remodelling. The aims of the PhD thesis are: 1. analysis of morphological (cellular or ultrastructural) and 2. functional (calcium metabolism, contractility) parameters of left ventricular myocytes from the experimental model of HF (transaortic banding in mice).

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Function of insulin-regulated aminopeptidase in development of metabolic syndrome.
Supervisor: Ing. Katarína Kršková, PhD.
Email: katarina.krskova@savba.sk
Keywords: Insulin resistance, obesity, adipogenesis, oxytocin, oxytocinase
Annotation: Insulin-regulated aminopeptidase (oxytocinase), IRAP, regulate glucose transport to cells in adipose tissue and skeletal muscle. On the other hand, its extracellular aminopeptidase activity degrades oxytocin, which in addition to its classical effects may also have positive metabolic (anti-obesity and anti-diabetic) effects.
The aim of this work is to investigate the role of IRAP in various adipose tissue subtypes and skeletal muscle in vivo in obese rats, as well as to elucidate the mechanisms of oxytocin action in vitro in the primary rat adipocyte culture, focusing on the insulin pathway and modulating adipocyte differentiation. For this purpose, the effect of inhibition of IRAP activity on glucose metabolism as well as the effect of application of selective oxytocin analogues on the anti-obesity and anti-diabetic activity in vitro and in vivo will also be investigated.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Regulation of preadipocyte differentiation and adipocyte metabolism by oxidative stress in rat and human tissue culture.
Supervisor: Ing. Štefan Zorad, CSc.
Email: Stefan.zorad@savba.sk
Keywords: adipogenesis, diabetes, adipose tissue, oxidtive stress, antioxidants, obesity, insulin resistance
Annotation: Fundamental molecular mechanisms of preadipocyte differentiation were almost exclusively studied on murine 3T3-L1 cell line. We developed our own method of rat subcutaneous preadipocyte differentiation and we will compare their adipogenic potential with commercial human subcutaneous preadipocytes. The effect of prooxidants and antioxidants on adipogenesis will be examined in both cultures. In addition, primary cultures prepared from subcutaneous adipose tissue from obese and diabetic rats will be examined. Insulin-stimulated glucose transport in rat and human mature adipocytes will be evaluated. Selected insulin postreceptor pathways related to differentiation and reactive oxygen species action will be studied. Obtained results might be applicable in humans mainly in relation to antioxidant usage for better health.

Study programm: Genetics
Form of study: daily (full-time)
Thesis: Identification of genes regulating apocrine secretion
Supervisor: RNDr. Robert Farkaš, CSc.
Email: ueenfark@savba.sk
Keywords: apocine secretion, intracellular transport, mechanism of externalization, genetic screening, protei-protein interactions
Annotation: Aims: Apocine secretion is Golgi-independent nonvesicular transport and secretory mechanism found only in metazoan eukaryotes. In contrast to well known exocytosis, it is poorly characterized noncanonical secretion. The aim of the project is identification of molecular determinants (genes and proteins) controling process of apocrine secretion and to uncover components of this novel signaling pathway.

Study programm: Genetics
Form of study: daily (full-time)
Thesis: The role of tumor suppressor genes and components of endoplasmic reticulum in hormone-triggered programmed cell death
Supervisor: RNDr. Robert Farkaš, CSc.
Email: ueenfark@savba.sk
Keywords: apocine secretion, intracellular transport, mechanism of externalization, genetic screening, protei-protein interactions
Annotation: Aims: Apocine secretion is Golgi-independent nonvesicular transport and secretory mechanism found only in metazoan eukaryotes. In contrast to well known exocytosis, it is poorly characterized noncanonical secretion. The aim of the project is identification of molecular determinants (genes and proteins) controling process of apocrine secretion and to uncover components of this novel signaling pathway.

Study programm: Genetics
Form of study: daily (full-time)
Thesis: Tumor-stroma interaction modelling in breast cancer and exploring its relevance in tumor progression and resistance
Supervisor: Mgr. Svetlana Miklíková, PhD.
Email: svetlana.miklikova@savba.sk
Keywords: Breast cancer, microenvironment, resistance, PDX models
Annotation: Breast cancer is the most common cancer in women worldwide. Despite its classification into well-recognized molecular subtypes, only some patients benefit from administering drug combinations. Dissecting the complex dynamics within tumor microenvironment are necessary for the identification of the physiological characteristics of non-responders vs. responders. The concept behind this project is integrating data from different experimental models, clinical trials and tumor molecular data at multiple levels for the identification of drivers of tumor progression and resistance.

Study programm: Microbiology
Form of study: daily (full-time)
Thesis: Host cell interaction with Coxiella burnetii: identification and utilization of novel therapeutic and diagnostic targets
Supervisor: Ing. Ľudovít Škultéty, DrSc.
Email: Viruludo@savba.sk
Keywords: Coxiella; effectors, proteins, small molecules, treatment, diagnostics
Annotation: Coxiella burnetii is an intracellular bacterial pathogen causing human infections of clinical and public health relevance. As many other bacterial pathogens, Coxiella uses specialized secretion systems to manipulate eukaryotic host cells by injection of effectors (bacterial virulence proteins and small molecules). However, current knowledge about how these pathogens establish infection is limited. The central research commitment of this project is the characterization of the functions of effector proteins from Coxiella burnetii. The project’s specific objectives include: 1) the description of the host cell signaling pathways targeted by effectors (proteins and small molecules) of Coxiella burnetii; 2) the characterization of the molecular and cellular mode of action of the effectors, and 3) a putative correlation between the mode of action of the effectors to their sequence variability and expression amongst different strains. The anticipated results may lead to the discovery of novel therapeutic approaches-drug targets- and could help in the design of vaccines and novel diagnostics. In particular, the host signaling pathways altered by one (or more) effector(s) will be promising candidates as novel therapeutic targets. Furthermore, the knowledge that will be gained could also lead to the identification of inhibitors targeting the pathogen’s effectors directly and help to design specifically drugs that can block the secretion system of the pathogen.

Study programm: Microbiology
Form of study: daily (full-time)
Thesis: Molecular analysis of the penetration of by vectors transmitted intracellular bacteria into cells, and their impact on the target cells.
Supervisor: RNDr. Zuzana Sekeyová, PhD.
Email: viruseke@savba.sk
Keywords: Rickettsiae, Coxiella burnetii, biomarkers, detection
Annotation: Intracellular bacteria are a constant source of scientific surprises. Their interaction, penetration into the target cells, proliferation, and the consequent biorhythm of infected cells were and they are continually being studied. They are partially described however, they are not completely explained nor understood. Today’s methods, based on modern instrumentation, allow the targeted view on a chain reaction of changes which occur after infection at the molecular level, thus, open up new horizons of knowledge.
The aim of the work is to reveal specific details about the biological activity and function of various bacterial (rickettsiae, Coxiella burnetii) and cellular structures (host); i.e. to create a picture of the “pathological mutations” of building blocks of both actors, of infectious and the infected organism, using the most advanced detection methods.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: Identification of genes regulating apocrine secretion
Supervisor: RNDr. Robert Farkaš, CSc.
Email: ueenfark@savba.sk
Keywords: apocine secretion, intracellular transport, mechanism of externalization, genetic screening, protei-protein interactions
Annotation: Aims: Apocine secretion is Golgi-independent nonvesicular transport and secretory mechanism found only in metazoan eukaryotes. In contrast to well known exocytosis, it is poorly characterized noncanonical secretion. The aim of the project is identification of molecular determinants (genes and proteins) controling process of apocrine secretion and to uncover components of this novel signaling pathway.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: The role of tumor suppressor genes and components of endoplasmic reticulum in hormone-triggered programmed cell death
Supervisor: RNDr. Robert Farkaš, CSc.
Email: ueenfark@savba.sk
Keywords: apocine secretion, intracellular transport, mechanism of externalization, genetic screening, protei-protein interactions
Annotation: Aims: Apocine secretion is Golgi-independent nonvesicular transport and secretory mechanism found only in metazoan eukaryotes. In contrast to well known exocytosis, it is poorly characterized noncanonical secretion. The aim of the project is identification of molecular determinants (genes and proteins) controling process of apocrine secretion and to uncover components of this novel signaling pathway.


 
 

Faculty of Chemical and Food Technology, Slovak University of Technology in Bratislava

 

Deadline for application: 15. 06. 2020

More information on website of the faculty here.

Study programm: Biochemistry
Form of study: daily (full-time)
Thesis: Disclosure of the molecular mechanism of spontaneous tumor regression: Development of novel prognostic tool
Supervisor: Ing. Ľudovít Škultéty, DrSc.
Email: Viruludo@savba.sk
Keywords: Mass spektrometry, proteomics, small molecules, diagnostics, lateral flow
Annotation: Spontaneous regression of tumor is a phenomenon that was reported in virtually all types of human malignancies. Recently, our team has observed this anti-tumor activity after high dose therapy and autologous stem cell transplantation in patients with Hodgkin’s disease, multiple myeloma, and some other malignancies. It seems to be associated with aplastic anemia like syndrome and ongoing pancytopenia induced by autoimmunity directed against hematopoietic stem cells. To understand the interconnected processes occurring in vivo we need to detect, identify, and structurally characterize clinically essential molecules involved in the depletion of tumor cells or tumors as a whole. We will therefore perform a systematic comparative proteomic analyses of control and treated (with polyclonal Abs of patients in regression/specific mAbs or other discovered target molecules) tumor cells. The obtained results will allow to reveal essential molecules associated with induction of tumor regression and recognize prognostic markers useful for monitoring the disease development. These finding will not only lead to a deeper understanding of this phenomenon at the molecular level, but in the link with novel information obtained from protein-protein interaction studies based on advanced proteomic analyses will contribute to future targeted therapy of certain malignancies and to design a valuable diagnostic tool for monitoring the progress of the disease.


 
 

Faculty of Science, Pavol Jozef Šafárik University in Košice

 

Deadline for application: no later than 30. 06. 2020

More information on website of the faculty here.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Activation of the endogenous mechanism in ischemic tolerance
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 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