PhD programs

PhD programs

Biomedical Research Center of the Slovak Academy of Sciences participates on PhD study of 4 Faculties of 3 Slovak Universities, it is an external educational institution of the following study programmes:

Faculty of Medicine
Comenius University in Bratislava
Normal and Pathological Physiology
Oncology
Faculty of Natural Sciences
Comenius University in Bratislava
Molecular Biology
Genetics
Microbiology
Animal Physiology
Biochemistry
Faculty of Chemical and Food Technology
Slovak University of Technology in Bratislava
Biochemistry
Faculty of Science
Pavol Jozef Šafárik University in Košice
Physiology of Animals
Biophysics

Theses for PhD study at the Biomedical Research Center of the Slovak Academy of Sciences for the academic year 2021/2022

 

Faculty of Natural Sciences, Comenius University in Bratislava

 

Deadline for application: 31. 05. 2021

More information on website of the faculty here.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: The role of the alternative renin-angiotensin system components in obesity and the development of metabolic disorders
Supervisor: Ing. Katarína Kršková, PhD.
Email: katarina.krskova@savba.sk
Keywords: Renin-angiotensin system, insulin resistance, obesityangiotensin-(1-7), angiotensin-converting enzyme 2, ACE2
Annotation: Obesity is a key risk factor for the development of the metabolic syndrome and its associated cardiovascular diseases and insulin resistance. The production of components of the classical renin-angiotensin system (RAS) is over-activated in obesity and increased angiotensin II production contributes to the pathogenesis of metabolic disorders. However, the current view of the RAS is becoming much more complex due to the discovery of the protective alternative pathways including angiotensin-converting enzyme 2 (ACE2), angiotensin- (1-7), Mas receptor and alamandine, opening up new possibilities in the search for a preventive and therapeutic strategy to regulate the pathogenesis of obesity and concomitant diseases. The aim of this work is to study these new alternative RAS pathways in order to investigate their role in the regulation of adipose tissue metabolism and insulin sensitivity, as well as the effect of modulating these pathways on anti-obese and anti-diabetic action in vitro and in vivo.

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: adipocyte differentiation, pro-oxidants, anti-oxidants, glucose, insulin, obesity
Annotation: Differentiation of preadipocytes to mature fat cells is one of the main mechanisms regulating the development of obesity and metabolic diseases. 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 which will be compared with human commercial preadipocyte differentiation. The effect of pro-oxidants (high concetration of glucose and TNFalpha) and anti-oxidants (e.g. flavonoids) is going to be examined in both cultures. In addition, primary cultures prepared from adipose tissue of obese and diabetic rats as well as selected insulin postreceptor pathways will be studied. Obtained results might be applicable in humans mainly in relation to anti-oxidant usage for better health.

Study programm: Genetics
Form of study: daily (full-time)
Thesis: Identification of molecular markers for early identification of pancreatic cancer
Supervisor: Mgr. Božena Smolková, PhD.
Email: bozena.smolkova@savba.sk
Keywords: pancreatic cancer, early diagnostics, biomarker, organoid, xenograft
Annotation: Slovakia is one of the countries with the highest incidence of pancreatic cancer. Due to the lack of treatment, early diagnosis is key to improving patient survival. The development and introduction of new models, including organoids and patient-derived xenografts, is an important tool for translational research. The dissertation will be partially realized within the NExT project, which aims to develop a microfluidic chip for the early detection of neuroendocrine pancreatic tumors. The aim of the dissertation thesis will be the identification of new diagnostic biomarkers. An important part will be the development of the above-mentioned preclinical models.

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: 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: ludovit.skultety@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. Like many other bacterial pathogens, Coxiella uses specialized secretion systems to manipulate eukaryotic host cells by injecting effectors (bacterial virulence proteins and small molecules). However, current knowledge about how these pathogens establish infection is limited. This project’s primary research commitment 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 gained could also lead to identifying inhibitors targeting the pathogen’s effectors directly and help design specific drugs that can block the pathogen’s secretion system.

Study programm: Microbiology
Form of study: daily (full-time)
Thesis: Differential diagnosis of Rickettsial diseases
Supervisor: Mgr. Marco Quevedo Diaz, PhD.
Email: marco.quevedo-diaz@savba.sk
Keywords: Rickettsiosis, Rickettsia, Rickettsialpox, epidemic tyfus, Rocky mountain spotted fever, Mediterranean spotted fever, Tibola.
Annotation: Rickettsiosis is a worldwide zoonosis, often endemic. Clinical signs include fever, nausea, rash, myalgia and lymphadenopathy. The course of the disease can be asymptomatic, mild to severe. The diagnosis of rickettsiosis consists in the direct detection of the pathogen in biological material by PCR or in the detection of specific antibodies in the blood serum by means of serological methods. We currently classify the genus Rickettsia into 4 groups: ancestral, typhus, spotted fever group and transitional group. The aim of this work is to identify potential biological markers capable of distinguishing the causative agents of individual rickettsiosis and to enable differential diagnosis of these diseases.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: Targeted manipulation of viral glycoprotein properties to restore immunity
Supervisor: Mgr. Ivana Nemčovičová, PhD.
Email: ivana.nemcovicova@savba.sk
Keywords: virus, glycoprotein, cellular receptor, protein interaction, immunomodulation, recombinant expression system, genetic manipulation, crystallization, structural analysis
Annotation: Viruses have evolved elegant mechanisms to evade detection by the host immune system. One of the evasion strategies that have been adopted by large DNA viruses is to encode homologues of endogenous molecules that have a crucial role in control of the immune response. The main thesis objective is to closely examine the molecular basis of immune recognition of clinically relevant glycoprotein encoded by human cytomegalovirus (HCMV). In this regard, we are planning a preparation, characterization, expression and purification of selected set of recombinant viral and human genes that are associated with cytotoxicity and viroprotectivity processes in the cell. The study of viral proteins could uncover the strategies of immune modulation that might have high therapeutic potential.

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) or external
Thesis: The role of the tumor microenvironment in histological subtypes of B cell non-Hodgkin lymphoma
Supervisor: RNDr. Jana Jakubíková, PhD.
Email: jana.jakubikova@savba.sk
Keywords: B non-Hodgkin lymphoma, the tumor microenvironment, resistance
Annotation: Immunophenotyping of haematological malignancies is a standard practice in clinical diagnosis and monitoring of the disease. Each lymphoma subtype is assigned to a unique stage of B cell differentiation and harbors certain genetic aberrations sustaining specific transformation and disease evolution. The aim of the PhD thesis is to understand role of the tumor microenvironment in lymphomagenesis with focus to define the effect of total host immunity on tumor cells, based on the study of various maturation stages of B-lymphocytes and other types of hematopoietic cells (T-lymphocytes, monocytes, granulocytes) and non-hematopoietic origin (stromal cells).

Study programm: Molecular Biology
Form of study: daily (full-time) or external
Thesis: The role of the immune system in the myeloma microenviroment
Supervisor: RNDr. Jana Jakubíková, PhD.
Email: jana.jakubikova@savba.sk
Keywords: multiple myeloma, immune system, the tumor microenvironment
Annotation: Multiple myeloma (MM), the second most common hematologic malignancy worldwide, is characterized by high frequency of intra-clonal diversity within malignant plasma cells in the bone marrow. A hallmark of the tumor microenvironment of MM is profound immune dysregulation and loss of immune surveillance, which contributes significantly to myeloma transformation and pathogenesis. The aim of the PhD thesis is to examine the overall immune system and their interactions with tumor cells in MM.

Study programm: Biochemistry
Form of study: daily (full-time)
Thesis: Targeted manipulation of viral glycoprotein properties to restore immunity
Supervisor: Mgr. Ivana Nemčovičová, PhD.
Email: ivana.nemcovicova@savba.sk
Keywords: virus, glycoprotein, cellular receptor, protein interaction, immunomodulation, recombinant expression system, genetic manipulation, crystallization, structural analysis
Annotation: Viruses have evolved elegant mechanisms to evade detection by the host immune system. One of the evasion strategies that have been adopted by large DNA viruses is to encode homologues of endogenous molecules that have a crucial role in control of the immune response. The main thesis objective is to closely examine the molecular basis of immune recognition of clinically relevant glycoprotein encoded by human cytomegalovirus (HCMV). In this regard, we are planning a preparation, characterization, expression and purification of selected set of recombinant viral and human genes that are associated with cytotoxicity and viroprotectivity processes in the cell. The study of viral proteins could uncover the strategies of immune modulation that might have high therapeutic potential.


 
 

Faculty of Science, Pavol Jozef Šafárik University in Košice

 

Deadline for application: will be announced

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

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Study of possibilities of functional recovery of injured neural pathways in laboratory rat
Supervisor: RNDr. Ján Gálik, CSc.
Email: galik@saske.sk
Keywords: traumatic injury, neural pathways, electrophysiology, electrical stimulation, axon growth
Annotation: The proposed theme of doctoral study includes:
– Study of mechanisms and models of traumatic injury of spinal cord and peripheral nerve.
– Understanding the principles and methods of electrophysiological recordings.
– Functional diagnosis of injured nerve pathways.
– Therapy based on application, or combination of methods of electrical stimulation, exercise and supportive pharmacological treatment.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: The development of translationally relevant regenerative and reparative strategies after spinal cord trauma
Supervisor: RNDr. Nadežda Lukáčová, DrSc.
Email: lukacova@saske.sk
Keywords: compression of the spinal cord, anti – inflammatory drugs, activation of pro-regenerative molecules
Annotation: The aim of PhD thesis is to investigate impact of anti-inflammatory drugs on the polarization of M1/M2 macrophages, which play a key role in activation of pro-regenerative molecules after traumatic spinal cord injury and to design strategies that have the potential to improve functional recovery of experimental animals. We plan to examine the protein profile in spinal cord after compression and application of methylprednisolone, atorvastatin and VX-210 and evaluate their neuroprotective potential. An innovative approach will be tested that will allow local application of the most effective drug to the site of injury via magnetic nanoparticles.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Pharmacologically induced modulation of inflammatory reaction and oxidative stress in acute phase after traumatic spinal cord injury
Supervisor: RNDr. Nadežda Lukáčová, DrSc.
Email: lukacova@saske.sk
Keywords: compression of the spinal cord, probiotics, siponimod, interaction intestine-spinal cord
Annotation: Traumatic spinal cord injury elicits inflammatory response that comprises the activation of resident cells (microglia and astrocytes) and the influx of cells of the immune system from the bloodstream to the site of injury (macrophages, neutrophils). Activation of microglia by pro-inflammatory mediators can convert astrocytes to the neurotoxic A1 phenotype. Macrophages can differentiate into cells that exacerbate tissue injury or promote CNS repair (M1 or M2 phenotype). The aim of Phd thesis is to find out, whether gut microbiome manipulation in the form of probiotics and siponimod is able to activate specific signalling pathways, M1/A2 activation and M1/M2 polarization.

Study programm: Biophysics
Form of study: daily (full-time)
Thesis: Targeted manipulation of viral glycoprotein properties to restore immunity
Supervisor: Mgr. Ivana Nemčovičová, PhD.
Email: ivana.nemcovicova@savba.sk
Keywords: virus, glycoprotein, cellular receptor, protein interaction, immunomodulation, recombinant expression system, genetic manipulation, crystallization, structural analysis
Annotation: Viruses have evolved elegant mechanisms to evade detection by the host immune system. One of the evasion strategies that have been adopted by large DNA viruses is to encode homologues of endogenous molecules that have a crucial role in control of the immune response. The main thesis objective is to closely examine the molecular basis of immune recognition of clinically relevant glycoprotein encoded by human cytomegalovirus (HCMV). In this regard, we are planning a preparation, characterization, expression and purification of selected set of recombinant viral and human genes that are associated with cytotoxicity and viroprotectivity processes in the cell. The study of viral proteins could uncover the strategies of immune modulation that might have high therapeutic potential.


 
 

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

 

Deadline for application: will be announced

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 a novel prognostic tool
Supervisor: Ing. Ľudovít Škultéty, DrSc.
Email: ludovit.skultety@savba.sk
Keywords: Mass spectrometry, proteomics, small molecules, diagnostics, lateral flow
Annotation: Spontaneous regression of a tumor is a phenomenon that was reported in virtually all types of human malignancies. Our team has recently 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. Therefore, we will perform 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 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 design a valuable diagnostic tool for monitoring the progress of the disease.

Study programm: Biochemistry
Form of study: daily (full-time)
Thesis: The role of the alternative renin-angiotensin system components in obesity and the development of metabolic disorders
Supervisor: Ing. Katarína Kršková, PhD.
Email: katarina.krskova@savba.sk
Keywords: Renin-angiotensin system, insulin resistance, obesityangiotensin-(1-7), angiotensin-converting enzyme 2, ACE2
Annotation: Obesity is a key risk factor for the development of the metabolic syndrome and its associated cardiovascular diseases and insulin resistance. The production of components of the classical renin-angiotensin system (RAS) is over-activated in obesity and increased angiotensin II production contributes to the pathogenesis of metabolic disorders. However, the current view of the RAS is becoming much more complex due to the discovery of the protective alternative pathways including angiotensin-converting enzyme 2 (ACE2), angiotensin- (1-7), Mas receptor and alamandine, opening up new possibilities in the search for a preventive and therapeutic strategy to regulate the pathogenesis of obesity and concomitant diseases. The aim of this work is to study these new alternative RAS pathways in order to investigate their role in the regulation of adipose tissue metabolism and insulin sensitivity, as well as the effect of modulating these pathways on anti-obese and anti-diabetic action in vitro and in vivo.

Study programm: Biochemistry
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. Katarína Kršková, PhD., Ing. Štefan Zorad, Csc.
Email: katarina.krskova@savba.sk, stefan.zorad@savba.sk
Keywords: adipocyte differentiation, pro-oxidants, anti-oxidants, glucose, insulin, obesity
Annotation: Differentiation of preadipocytes to mature fat cells is one of the main mechanisms regulating the development of obesity and metabolic diseases. 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 which will be compared with human commercial preadipocyte differentiation. The effect of pro-oxidants (high concetration of glucose and TNFalpha) and anti-oxidants (e.g. flavonoids) is going to be examined in both cultures. In addition, primary cultures prepared from adipose tissue of obese and diabetic rats as well as selected insulin postreceptor pathways will be studied. Obtained results might be applicable in humans mainly in relation to anti-oxidant usage for better health.