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 Physical Education and Sport
Comenius University in Bratislava
Sports Educology
Sports Kinanthropology
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 2022/2023

 

Faculty of Science, Pavol Jozef Šafárik University in Košice

 

Deadline for application: 31. 5. 2022

More information on website of the faculty here.

Study programm: 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


 

Faculty of Natural Sciences, Comenius University in Bratislava

 

Deadline for application: 31. 05. 2022

More information on website of the faculty here.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: The effect of training on the cardiac function in obese rats
Supervisor: RNDr. Alexandra Zahradníková ml., PhD.
Email: saschia.zahradnikova@savba.sk
Keywords: Obesity, heart, physical activity, running
Annotation: Physical activity is one of the natural mechanisms used in prevention and reduction of obesity. Physical training is also beneficial in patients with heart failure. The aim of the study is to evaluate the effect of structured training and spontaneous physical activity on the functional parameters of the cardiovascular system and morphological and molecular changes in cardiac myocytes.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Mitochondrial morphology and function in experimental models of heart failure and Wolfram syndrome
Supervisor: RNDr. Michal Cagalinec, PhD.
Email: michal.cagalinec@savba.sk
Keywords: Mitochondria, heart failure, Wolfram syndrome, confocal microscopy, electron microscopy
Annotation: Mitochondria are key organelles both in terms of energy production and intracellular signaling. Disruption of these processes in pathological condition such as heart failure, but also rare genetic disorders such as Wolfram’s syndrome is associated with changes in mitochondria metabolism, dynamics and morphology. All these factors significantly affect the course and prognosis of these diseases. The aim of this work is to use modern methods of confocal and electron microscopy to determine the function and morphology of mitochondria in experimental models of heart failure, Wolfram syndrome and others.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Investigating the role of GPR180 signaling in beta cell function and pathogenesis of diabetes
Supervisor: Mgr. Lucia Balážová, PhD.
Email: lucia.balazova@savba.sk
Keywords: diabetes, pancreatic beta cells, insulin secretion, GPR180, CTHRC1
Annotation: Identification of novel strategies to control glycaemia is of interest given the alarming prevalence of diabetes. The aim of the project is to study the role of GPR180 receptor and its ligand CTHRC1 in regulation of pancreatic cytoarchitecture and ß cell function focusing on the mechanism of insulin secretion. Phenotyping of ß cell specific GPR180 knockout mice complemented by functional in vitro studies will enable to identify the significance of this signalling pathway. Part of the experimental work can be carried out at ETH Zurich (Switzerland) in laboratory of prof. Wolfrum if the doctoral student receives scholarship for reaserch mobility.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Neurobiological basis of mental diseases: hormonal dysregulations
Supervisor: RNDr. Nataša Hlaváčová, PhD.
Email: natasa.hlavacova@savba.sk
Keywords: Mood disorders, neuroendocrine system, stress, animal models
Annotation: The PhD thesis will be focused on the study of regulatory mechanisms underlying the development of mental disorders, especially depression and schizophrenia. Research will be conducted both in human and animal studies to find new knowledge for better prevention and treatment of mood disorders. Atypical effects of hormones such as aldosterone, oxytocin, copeptin, testosterone will be investigated. In addition to neuroendocrine mechanisms and atypical effects of hormones on brain functions, indicators of brain plasticity and neurogenesis, whose changes contribute to the development of mental disorders, will be studied.

Study programm: Animal Physiology
Form of study: daily (full-time)
Thesis: Modulation o endocannabinoid system as a as a promising target for the treatment of stress-related psychiatric disorders
Supervisor: RNDr. Nataša Hlaváčová, PhD.
Email: natasa.hlavacova@savba.sk
Keywords: mood disorders, stress, endocannabinoid system, animal models
Annotation: The PhD thesis will be focused on investigatation of effect of pharmacological modulation of the endocannabinoid (eCB) system in
the prevention of psychopathological consequences of chronic stress and to identify neurobiological mechanisms involved. Experimental approaches will employ animal models of stress and pharmacological enhancement of
eCB signaling. Behavioral changes in a battery of behavioral tests, changes in the neuroendocrine system, inflammatory markers, and epigenetic factors will be assessed. Indicators of brain plasticity and neurogenesis, the changes of which contribute to the development of mental disorders, will also be monitored.

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 cardiometabolic disorders
Supervisor: Ing. Štefan Zorad, CSc.
Email: stefan.zorad@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 cardiovascular diseases and metabolic syndrome. Over-activation of the classical renin-angiotensin system (RAS) 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 the work is to study the new alternative RAS pathways and investigation of their cardiometabolic effects by modulation of these pathways in vitro and in vivo to elucidate the role of ACE2 and Mas receptor in the pathogenesis of obesity and diabetes.

Study programm: Genetics
Form of study: daily (full-time)
Thesis: Identification of genes regulating apocrine secretion
Supervisor: RNDr. Robert Farkaš, CSc.
Email: robert.farkas@savba.sk
Keywords: apocine secretion, intracellular transport, mechanism of externalization, genetic screening, protein-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: Reprogramming pancreatic ductal adenocarcinoma microenvironment towards imunotherapy
Supervisor: Mgr. Božena Smolková, PhD.
Email: bozena.smolkova@savba.sk
Keywords: pancreatic ductal adenocarcinoma, tumor microenvironment, reprogramming, immunotherapy, epigenetic drugs, combination therapy
Annotation: Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease with a 5-year survival below 10%. Although immune checkpoint inhibitors revolutionized cancer treatment, PDAC patients still do not benefit from immune therapies. This lack of response mainly resides in the low immunogenicity and non-inflamed nature of PDAC that can be predicted, in part, from the immune phenotypes present in the tumor microenvironment (TME). The main goal of the thesis is understanding of the complexity and heterogeneity of PDAC TME by identification of critical TME elements driving PDAC progression and response to therapy and introduce new targetable TME components. This approach allows exposing new vulnerabilities that will inform the design and testing of more effective combinatorial approaches in preclinical platforms.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: Development of a Lateral flow assay for Q fever
Supervisor: Mgr. Gabriela Flores-Ramírez, PhD.
Email: gabriela.flores-ramirez@savba.sk
Keywords: Q fever, Coxiella burnetti, diagnostic
Annotation: Lateral flow assays (LFAs) are rapid diagnostic devices that can be used to test for a target substance (antigen) in a sample (saliva, sera or blood). Nowadays are widely use in the health and veterinary system fields. Some of the advantages to the LFA are that these assays have a long shelf life, do not require refrigerated storage, can handle small volumes of antigen and sample, can have high sensitivity, specificity and stability, it does not need extensive training for using it and it have a relative low cost for development. Coxiella burnetii causes Q fever. During the last decade, several outbreaks in Europe of the illness occurred causing both, economical losses in the livestock industry and the spread of the infection in humans. Due to their similar symptoms with commonly bacterial infections and its clinical diagnosis requires time and special methods. In here, we propose a)to study the immunoreactive secreted proteins and b) to develop an optimize a lateral flow assay for Q fever.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: Warranty of blood safety towards mosquito-borne viruses infections in the era of global change
Supervisor: RNDr. Viktória Čabanová, PhD.
Email: viktoria.cabanova@savba.sk
Keywords: Blood safety, mosquito-borne viruses, West Nile virus, Usutu virus, mosquitoes
Annotation: Number of mosquito-borne viral infections is steadily increasing in Europe. This phenomenon is obviously triggered by a changing environment, a direct human impact, altogether named as a global change. In Europe, West Nile (WNV) and Usutu (USUV) virus infections have the greatest impact on public health. The majority of cases are asymptomatic, but in some situation, an infection can develop to a neuroinvasive disease and for some patients can be even fatal. A number of WNV and USUV infections transmitted by transfusion of infected blood and transplantation were reported worldwide. In a year in Europe, around 25 million blood transfusions are used to save someone’s life. The great effort to save those people can be defeated by an acquired WNV/USUV infection via transfusion. Warranty of blood safety against WNV and USUV became one of the highest priorities in blood transfusion service in Europe. But to be able to eliminate the risk, several steps need to be implemented. During the project, we will perform blood donors screening with collaboration of transfusion services in already investigated foci of WNV and USUV. Likewise, a virus surveillance among vector population will be done to obtain more detailed data about virus seasonality, which can help to reduce cost for future donor screening. For better understanding of different development of WNV and USUV in some patients, a genetic characteristic by NGs and a virus toxicity to a cell cultures will be studied. Additionally, the study of insecticide resistance will be performed in all sampling areas because this increasing phenomenon can change whole perspective in handling of these MBV.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: Study on the use of virokines in immunotherapy of cancer
Supervisor: RNDr. Katarína Lopušná, PhD.
Email: katarina.lopusna@savba.sk
Keywords: Virokines, immuntherapy, tumors
Annotation: Virokines are soluble proteins homologous to cytokines, they are produced by host cell infected by viruses as immune evasion mechanism to suppress the host immune response. It is known that not only healthy cells of immune system, but also tumor cells express receptors which are recognized by virokines. The aim of this study is to identify new potential virokines using bioinformatical methods as well as the study of the use of virokines in immunotherapy of cancer.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: Development of novel diagnostic and predictive immunophenotyping tool for hematological malignancies
Supervisor: RNDr. Jana Jakubíková, PhD.
Email: jana.jakubikova@savba.sk
Keywords: hematological malignancies, immunophenotyping, mass cytometry
Annotation: Immunophenotyping is currently one of the fundamental pillars for the diagnosis, classification, staging and monitoring of hematological malignancies, such as leukemia and lymphoma. In this study, we will take an advantage of novel high-dimensional technology mass cytometry that to develop novel diagnostic and predictive approach with complex multi-dimensional immunophenotyping profiles and overall immune cell profiling to diagnose, classify, stage and monitor of the therapy response in patients with leukemia, lymphoma and multiple myeloma.

Study programm: Molecular Biology
Form of study: daily (full-time)
Thesis: Evaluation of immune checkpoints in B cell malignancies
Supervisor: RNDr. Danka Cholujová, PhD.
Email: dana.cholujova@savba.sk
Keywords: B cell lymphomas, immunophenotyping, mass cytometry
Annotation: Malignant lymphomas are mostly incurable blood cancers affecting different white blood cells formed in lymphoid structures, including the lymph nodes, spleen, and bone marrow. They have different origin in B cell development with different biological properties and clinical aggressiveness. In this study, we will analyze the immunological mechanisms “immune checkpoints” that can be targeted in malignant lymphoma. The better understanding of pathogenesis of B-cell malignancies will lead to new therapeutic strategies directed against tumor and immune cells to completely eradicate tumor in individual patient.

Study programm: Microbiology and Virology
Form of study: daily (full-time)
Thesis: Genomic and proteomic studies of vector-borne microorganisms in their vectors and hosts
Supervisor: Mgr. Eva Špitalská, PhD.
Email: eva.spitalska@savba.sk
Keywords: vector, vector-borne microorganisms, photodynamic therapy, genomic, proteomic
Annotation: Analysis of vectors and vector-borne microorganisms in vectors and hosts. Monitoring of effects of photodynamic therapy on infections caused by vector-borne microorganisms in vivo, in vitro and changes on genomic and proteomic level.

Study programm: Microbiology and Virology
Form of study: daily (full-time)
Thesis: Development of a Lateral flow assay for Q fever
Supervisor: Mgr. Gabriela Flores-Ramírez, PhD.
Email: gabriela.flores-ramirez@savba.sk
Keywords: Q fever, Coxiella burnetti, diagnostic
Annotation: Lateral flow assays (LFAs) are rapid diagnostic devices that can be used to test for a target substance (antigen) in a sample (saliva, sera or blood). Nowadays are widely use in the health and veterinary system fields. Some of the advantages to the LFA are that these assays have a long shelf life, do not require refrigerated storage, can handle small volumes of antigen and sample, can have high sensitivity, specificity and stability, it does not need extensive training for using it and it have a relative low cost for development. Coxiella burnetii causes Q fever. During the last decade, several outbreaks in Europe of the illness occurred causing both, economical losses in the livestock industry and the spread of the infection in humans. Due to their similar symptoms with commonly bacterial infections and its clinical diagnosis requires time and special methods. In here, we propose a)to study the immunoreactive secreted proteins and b) to develop an optimize a lateral flow assay for Q fever.

Study programm: Microbiology and Virology
Form of study: daily (full-time)
Thesis: Warranty of blood safety towards mosquito-borne viruses infections in the era of global change
Supervisor: RNDr. Viktória Čabanová, PhD.
Email: viktoria.cabanova@savba.sk
Keywords: Blood safety, mosquito-borne viruses, West Nile virus, Usutu virus, mosquitoes
Annotation: Number of mosquito-borne viral infections is steadily increasing in Europe. This phenomenon is obviously triggered by a changing environment, a direct human impact, altogether named as a global change. In Europe, West Nile (WNV) and Usutu (USUV) virus infections have the greatest impact on public health. The majority of cases are asymptomatic, but in some situation, an infection can develop to a neuroinvasive disease and for some patients can be even fatal. A number of WNV and USUV infections transmitted by transfusion of infected blood and transplantation were reported worldwide. In a year in Europe, around 25 million blood transfusions are used to save someone’s life. The great effort to save those people can be defeated by an acquired WNV/USUV infection via transfusion. Warranty of blood safety against WNV and USUV became one of the highest priorities in blood transfusion service in Europe. But to be able to eliminate the risk, several steps need to be implemented. During the project, we will perform blood donors screening with collaboration of transfusion services in already investigated foci of WNV and USUV. Likewise, a virus surveillance among vector population will be done to obtain more detailed data about virus seasonality, which can help to reduce cost for future donor screening. For better understanding of different development of WNV and USUV in some patients, a genetic characteristic by NGs and a virus toxicity to a cell cultures will be studied. Additionally, the study of insecticide resistance will be performed in all sampling areas because this increasing phenomenon can change whole perspective in handling of these MBV.

Study programm: Microbiology and Virology
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: Biochemistry
Form of study: daily (full-time)
Thesis: The role of the alternative renin-angiotensin system components in obesity and the development of cardiometabolic 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 cardiovascular diseases and metabolic syndrome. Over-activation of the classical renin-angiotensin system (RAS) 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 the work is to study the new alternative RAS pathways and investigation of their cardiometabolic effects by modulation of these pathways in vitro and in vivo to elucidate the role of ACE2 and Mas receptor in the pathogenesis of obesity and diabetes.


 

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

 

Deadline for application: 31. 05. 2022

More information on website of the faculty here.

Study programm: Biochemistry
Form of study: daily (full-time)
Thesis: Development of a Lateral flow assay for Q fever
Supervisor: Mgr. Gabriela Flores-Ramírez, PhD.
Email: gabriela.flores-ramirez@savba.sk
Keywords: Q fever, Coxiella burnetti, diagnostic
Annotation: Lateral flow assays (LFAs) are rapid diagnostic devices that can be used to test for a target substance (antigen) in a sample (saliva, sera or blood). Nowadays are widely use in the health and veterinary system fields. Some of the advantages to the LFA are that these assays have a long shelf life, do not require refrigerated storage, can handle small volumes of antigen and sample, can have high sensitivity, specificity and stability, it does not need extensive training for using it and it have a relative low cost for development. Coxiella burnetii causes Q fever. During the last decade, several outbreaks in Europe of the illness occurred causing both, economical losses in the livestock industry and the spread of the infection in humans. Due to their similar symptoms with commonly bacterial infections and its clinical diagnosis requires time and special methods. In here, we propose a)to study the immunoreactive secreted proteins and b) to develop an optimize a lateral flow assay for Q fever.

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 cardiometabolic disorders
Supervisor: Ing. Štefan Zorad, CSc.
Email: stefan.zorad@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 cardiovascular diseases and metabolic syndrome. Over-activation of the classical renin-angiotensin system (RAS) 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 the work is to study the new alternative RAS pathways and investigation of their cardiometabolic effects by modulation of these pathways in vitro and in vivo to elucidate the role of ACE2 and Mas receptor in the pathogenesis of obesity and diabetes.

Study programm: Biochemistry
Form of study: daily (full-time)
Thesis: Identification and characterization of processes of bacterial adaptation using omics technologies
Supervisor: Ing. Ľudovít Škultéty, DrSc.
Email: ludovit.Skultety@savba.sk
Keywords: mass spectrometry, proteomics, small molecules, bacterial adaptation
Annotation: Bacteria belong to microorganisms that are spread widely on the planet. In nature, they mainly inhabit the soil. Herein, they form communities that participate in the transformation of many substances. They can decompose dead bodies of plants and animals as well as convert many pollutants (including aromatic hydrocarbons) into substances usable by higher plants. Some bacteria, however, depend on others, usually higher organisms (plants, animals, humans). According to their relationship to host, they can be symbiotic (mutually beneficial), pathogenic (causing diseases), or live together with the macroorganism but do not affect it in any way. To “survive,” bacteria undergo significant phenotypic and genotypic changes.
The main aim of the Ph.D. study is to understand the processes associated with bacterial adaptation. The student will perform a systematic comparative analysis of control and adapted cells of selected bacterial isolates, using omics methodologies such as proteomics, metabolomics, and transcriptomics. The data obtained will then allow recognition of essential molecules responsible for the activation of their metabolism.