Projects
CAMO3E Project
Advanced imaging in the early diagnosis of esophageal tumours
Project code: 401101F618
Acronym: CAMO3E
The CAMO3E project is focused on the development and verification of innovative multimodal imaging approaches for the early diagnosis of esophageal tumors. Through the integration of advanced optical and biophotonic technologies, artificial intelligence methods and preclinical models, it creates a platform for the identification of new imaging biomarkers and the improvement of diagnostic procedures. The project will contribute to the development of cutting-edge biomedical research at Pavol Jozef Šafárik University in Košice, strengthen its research infrastructure in the field of advanced imaging and support international cooperation in research, development and innovation. The results of the project will create the prerequisites for a more efficient transfer of modern diagnostic technologies to clinically oriented research and personalized medicine. The project is co-supported from the European Union through Programme Slovakia: Support for international cooperation in the field of research, development and innovation – Healthy Society Domain.
Principal investigator: RNDr. Veronika Huntošová, PhD.
Project duration: 01/07/2026 – 30/06/2028
BioPickmol
Development of Nanosensor-Based Photonic Systems for Rapid Virus Detection 
Using Directed Evolution of Protein Scaffolds: The Case of SARS-CoV-2
The project focuses on functionalising the surface of a detection chip with a nanoscale layer of specific binding proteins developed through the directed evolution of selected protein scaffolds. Protein nanolayers will be assembled on the chip using controlled, site-specific chemical conjugation to optimise binding efficiency and ensure reproducible detection performance. Following application of a sample containing inactivated virus to the functionalised chip, viral particles will be detected using surface-enhanced Raman spectroscopy (SERS), with signal enhancement mediated by surface plasmons. A dedicated detection system, bioRAMASCOPE, will be developed to acquire signals from the functionalised chips. The system will be designed to meet the specific detection limit and operational reliability requirements for SARS-CoV-2 detection. Advanced selection methods in protein engineering will be used to develop engineered proteins as novel biological entities capable of specifically binding inactivated viruses. By combining proteins that recognise distinct epitopes, we aim to achieve highly sensitive and specific detection of different viruses, including SARS-CoV-2.
Project guarantor: UPJŠ, doc. RNDr. Gabriel Žoldák, PhD.
Period: 01/2021 – 06/2023
OPENMED
Open Scientific Community for Modern Interdisciplinary Research in Medicine (OPENM
ED)
Project OPENMED (participants: University of P.J. Šafárik in Košice (UPJŠ), Technical University of Košice (TUKE), University of Veterinary Medicine and Pharmacy (UVLF), Neurobiological Institute of the Biomedical Center SAV (NbÚ BMC SAV) and two partners from industrial sector – MM MEDICAL s.r.o. and JUHAPHARM s.r.o.) set as priority goals to solve selected problems of diagnosis and treatment of oncological, cardiovascular and viral diseases, CNS diseases as well as diseases of the musculoskeletal system. The uniqueness and originality of the OPENMED project lies in the meaningful use of the multidisciplinary environment of the universities in Košice and scientific research facilities, which are connected by complementary expertise in the fields of medicine, natural and technical sciences, and veterinary medicine. This connection, combined with an ambitious intention for technological transfer, represents a unique ecosystem of biomedical research in Slovakia. The intensive interdisciplinary cooperation between the project partners resulted in the creation of modern research areas connecting individual new biomedical fields, namely: i) nanomedicine and targeted therapy, ii) personalized medicine and iii) regenerative medicine and cell therapy. The overall goal of the project, the creation of a unique eco-system in the OPENMED consortium consisting of complementary scientific-research biomedical infrastructure and highly qualified professional personnel, will lead to the improvement of diagnostic and therapeutic approaches in the treatment of the above-mentioned serious civilizational diseases through the application of the obtained research results in practice, and thus also to improve the health status of the population.
Project guarantor: doc. Mgr. Daniel Jancura, PhD.
Period: 1.11.2019 – 30.6.2023
CasProt
Fostering high scientific quality in protein science in Eastern Slovakia (CasProt)
Project objective: The main goal of the project is to increase the scientific capacity and grow the research potential of UPJŠ in Košice in the field of protein sciences. Its implementation will take 3 years. Top research teams of partner entities of the Technical University of Munich and the University of Zurich participate in the project. This project will lead to the development of technologies and the increase of the innovation potential of UPJŠ in Košice with the expected impact not only on eastern Slovakia but also on the whole country.
The results of the research will provide an understanding of the molecular basis of the regulation of GPCR function, as well as the improvement of a rational approach to the targeted development of new drugs. The project also significantly supports young scientists in the development of skills in the field of interdisciplinary biosciences, and one of the ambitions of the project is also to attract back experienced Slovak scientists working abroad for a long time. It is expected that the results of the project will lead to the creation of a patent and start-up company as well as to contacts with major industrial companies.
CELIM
The project 7FP EU (REGPOT) „Fostering Excellence in Multiscale Cell Imaging“ (CELIM) is designed to energize the research potential of the University of P. J. Safarik in Kosice, Slovakia, by the enhancement of the existing network of collaborators with the selected excellent European Partners, centered around the theme of cell imaging, by the acquisition of a new technical infrastructure, and by the reintegration of highly experienced Slovak scientists contemporary working abroad.
The advanced protein biotechnology consortium: A model for fostering economic growth and mitigating brain drain in Eastern Slovakia
Project code: 09I02-03-V01-00021
Akronym/Acronym: APBC
The Advanced Protein Biotechnology Consortium is a project aimed at an international collaborative R&D model with excellent academic partners to address economic and social challenges in Slovakia while effectively mitigating the brain drain from Eastern Slovakia. The APBC project is strategically designed to foster sustainable development by leveraging the potential of protein biotechnology, setting up the conditions for the creation of intellectual property in the given area and the conditions to attract bio-production facilities in the long term. By focusing on this cutting-edge field, the consortium aims to drive economic growth, create high-skilled job opportunities, and enhance the overall competitiveness of Slovakia in the bio-industrial segment. Hence, APBC provides a model proof-of-principle concept for addressing the significant challenges in Slovakia, and we expect that our initiative will motivate other industrial segments as well.
Principal investigator: prof. RNDr. Erik Sedlák, DrSc.
Period: 03/2025-08/2027
Exploring the structural properties and therapeutic potential of the Hsp70 chaperone’s substrate-binding domain for the treatment of amyloidosis
Project code: 09I03-03-V04-00116
Amyloidosis is a group of diseases characterized by the improper folding and aggregation of light chain, leading to their deposition in various tissues. This impairs their functionality and results in serious health complications. Despite the severity of amyloidosis, there is currently no effective treatment aimed at suppressing light chain aggregation. In this project, we plan to elucidate the structural properties and therapeutic potential of the substrate-binding domain of the chaperone Hsp70 as a novel strategy to combat amyloidosis. To achieve this, we will employ a combination of molecular biology, biophysics, and structural biology techniques. The added value of the project lies in the establishment of protein crystallography as a new scientific discipline at UPJS, both at practical and theoretical levels.
Principal Investigator: RNDr. Michal Nemergut, PhD.
Period: 07/2024 – 06/2026
Breast cancer organoid on a chip for fluorescence lifetime imaging of autophagy and apoptosis induced by targeted treatment with designed ankyrin repeat protein
Project code: 09I03-03-V04-00007
Fluorescence lifetime is a unique parameter of a molecule that is very sensitive to the environment. Therefore, fluorescence lifetime imaging allows identification of local changes in cells with high spatial and temporal resolution. Replacing animal models for human disease is a high priority in our research. This project aims to create a breast cancer organoid composed of cells with various expression of human epidermal growth factor receptor 2 to monitor subcellular and cellular interactions during targeted treatment. The organoid thus exhibits a high degree of heterogeneity and bridges the gap between cell cultures and in vivo models of cancer. The innovative approach of a hydrogel scaffold of recombinant spider silk proteins is proposed to grow cells on a chip. The cells on the chip are targeted by a nano-delivery system consisting of metal-based nanoparticles and a designed ankyrin repeat protein. The composition of the nanoparticles enables multimodal bioimaging and treatment.
Principal Investigator: RNDr. Veronika Huntošová, PhD.
Period: 07/2024 – 06/2026
Rational design of stable and catalytically effective haloalkane dehalogenase DhaA
Project code: 09I03-03-V04-00112
Haloalkane dehalogenases (HLDs) are known as microbial enzymes that can degrade synthetic halogenated compounds that are recognized as pollutants. Three archetypal enzymes (DhlA, DhaA, and LinB) have been extensively studied and modified by protein engineering. However, obtaining biotechnology-required qualitative traits of HLDs still represents a significant obstacle for researchers. This project brings original solution for possible enhancement of stability and catalytic activity of a group of haloalkane dehalogenases. The major achievement will be establishment of methodology for effective improvement of HLD by combination of methods of the rational design and protein evolution. To demonstrate efficiency of the proposed approach, well-characterized haloalkane dehalogenase DhaA will be chosen as a HLD representative.
Principal investigator: RNDr. Ivana Timková, PhD.
Period: 9/2024-6/2026
ExCasProt
Podpora rozvoja biotechnologického výskumu proteínov na východnom Slovensku
Fostering high scientific quality in protein research in Eastern Slovakia
Kód projektu: 09I01-03-V04-00041
Hlavým cieľom predkladaného projektu ExCasProt je pomocou metód riadenej evolúcie vyvinúť a identifikovať solubilné analógy GPCR proteínov, čo povedie k jednoduchšej manipulácii s nimi, lepšiemu pochopeniu ich štruktúry a funkcie.
Receptory spojené s G-proteínmi (GPCR) predstavujú dôležitú skupinu membránových proteínov. V organizme zohrávajú kľúčovú úlohu a narušenie ich signálnej dráhy je spojené s množstvom ochorení, preto sú relevantným cieľom farmaceutického priemyslu. Dizajn liečiv založený na detailnom poznaní štruktúry komplexov proteín-ligand je jedným z najefektívnejších prístupov v súčasnom výskume liekov. U GPCR je počet dostupných štruktúr obmedzený v dôsledku nedostatku štruktúrnych údajov spôsobených komplikáciami súvisiacimi s ich produkciou a izoláciou v natívnej forme. Hlavým cieľom predkladaného projektu ExCasProt je pomocou metód riadenej evolúcie vyvinúť a identifikovať solubilné analógy GPCR proteínov, čo povedie k jednoduchšej manipulácii s nimi, lepšiemu pochopeniu ich štruktúry a funkcie. Úspech v konkrétnom prípade nám poslúži ako dôkaz princípu, ktorý by mohol byť aplikovateľný aj na ďalšie proteíny z triedy GPCR.
Hlavný riešiteľ: Mgr. Mária Tomková, PhD.
Doba trvania projektu: 2/2024 – 6/2026
Development of luciferase with increased brightness using a yeast bioluminescent system 
Project objective: This project aims to develop a new luciferase variant with improved luminescence that can compete with existing commercially available luciferases. The innovation consists in the directed evolution of a luciferase isolated from the fungus Neonothopanus nambi, which is the only known eukaryotic luciferase with an identified metabolic pathway for the synthesis of its natural substrate. To achieve this goal, it is planned to develop a genetically modified yeast bioluminescent system that will allow the production of the corresponding substrate and the monitoring of the interaction between the luciferase and the substrate directly in the yeast.
Principal investigator: RNDr. Michal Nemergut, PhD.
Period: 1/2025 – 12/2027
Development and Optimisation of a Bacterial Expression System for Pathological Forms of the Human Immunoglobulin G (IgG) Light Chain (VEGA 1/0024/22)
Bacterial production of recombinant proteins plays an important role in basic research aimed at understanding the molecular basis of pathological forms of human proteins. In addition to their use in research, these recombinant proteins are required for the efficient development of diagnostic platforms. The availability of a wide range of suitable expression vectors, together with the ease of cultivating E. coli, enables scalable protein production. In the first stage of this project, we will focus on optimising the expression of publicly available pathological forms of the immunoglobulin G light chain in E. coli. In the second stage, we will use molecular biology techniques to generate new tandem protein constructs containing a pathological light chain covalently linked to a protein belonging to the group of so-called solubility-enhancing tags. By investigating the effects of five different solubility enhancers (SUMO, MBP, SlyD, GB1 and GST) on light-chain expression levels, we will establish an optimal bacterial expression system.
Principal investigator: UPJŠ, doc. RNDr. Gabriel Žoldák, DrSc.
Period: 01/2022 – 12/2024
Study and modification of properties of spider protein overexpressed in Escherichia coli
Project objectives: 1) to establish controllable “bottom-up” self-assembly of spider protein; and 2) to engineer spider-amyloid based nanocomposites for biomedical and biotechnological applications. The project is result of a collaboration with the group of RNDr. Ing. Katarína Šipošová, PhD. from Slovak Academy of Sciences.
Principal investigator: doc. RNDr. Erik Sedlák, DrSc.
Period: 2022-2025
Modification of catalytic properties of haloalkane dehalogenases by protein evolution methods
Project objectives: To develop stable HLDs analogues, characterized by catalytic properties suitable for biotechnological applications by the method of directed evolution of proteins – ribosome display.
Principal investigator: doc. RNDr. Erik Sedlák, DrSc.
Period: 2022-2024
Aggregation of immunoglobulins and prediction of their colloidal stability using advanced kinetic analysis
Project objective: Stability of immunoglobulins G (IgGs) is one of the most critical properties affecting the success of the clinical application of immunotherapeutics. Obtaining correct parameters which describe the stability and aggregation of IgG is certainly a very ambitious goal mostly due to the complexity of their structures. In this project, our group will develop a biophysical model, which will be based on the analysis of IgG inactivation kinetics and microcalorimetry at elevated temperatures.
Principal Investigator: RNDr. Gabriel Žoldák, PhD.
Period: 2019–2022
Time-resolved imaging of oxygen consumption in cancer cells during photo-dynamic therapy
Project objective: The main aim of this project is focused on implementation of time-resolved measurements for the analysis of metabolic processes during photo-dynamic therapy (PDT) of cancerous diseases. The motivation and aims are built on expertise and scientific skills of the team members achieved in the field of time-resolved microscopy and spectroscopy and new approaches for image processing (bootstrap and statistical morphology). The particular aims of this project are: a) to characterize Stern-Volmer calibration curves of PpIX and RuPhen in the solution by time-resolved methods, b) to follow subcellular distribution of PpIX and RuPhen after PDT and to define the therapeutical protocol, c) to construct oxygenation maps of PDT treated cancer cells by PpIX or RuPhen calibration curves and PpIX or RuPhen luminescence lifetimes detected in live cells. We will use a unique set-up for fluorescence and phosphorescence lifetime measurements in real time available at CIB and KBF at UPJŠ in Košice: FLIM/PLIM microscopy system.
Principal Investigator: RNDr. Veronika Huntošová, PhD.
Period: 2018-2020
Directed evolution of haloalkane dehalogenases with enhanced activity 
and stability using ribosome display
Project objective: Haloalkane dehalogenases (HLDs) are hydrolase enzymes that catalyze the cleavage of carbon–halogen bonds, thereby converting toxic halogenated compounds into less harmful substances. Enzyme-mediated dehalogenation has wide applications in industry and significant potential for the bioremediation of common environmental pollutants. However, the practical use of HLDs is limited by factors such as insufficient thermal stability and low catalytic efficiency of naturally occurring enzymes. These complex enzyme properties can be improved using efficient directed protein evolution strategies. The aim of this project is to develop stable HLD variants with catalytic properties suitable for biotechnological applications. To achieve this goal, we will employ ribosome display as a powerful method of directed protein evolution. The selected HLD variants will be further characterized to elucidate the effects of acquired mutations on enzyme stability and catalytic performance.
Principal Investigator: RNDr. Michal Nemergut, PhD.
Period: 2026-2030
Development of efficient genetically encoded photosensitizers
Project objective: The principal goal of this project is to develop a molecular method by which we will be able to transform unrelated flavoproteins into efficient photosensitizers producing singlet oxygen with a high quantum yield.
Principal Investigator: doc. RNDr. Erik Sedlák, DrSc.
Period: 2021–2025
Understanding IgG inactivation mechanism using single Hsp70 chaperone molecules and laser optical tweezers (Hsp70sensor)
Project objective: Structural and biochemical complexity of IgGs, as well as unclear inactivation mechanism, provide a significant hurdle for their accelerated development and their use in the clinical applications. In particular, the major concern during early stages of research and development is a natural tendency of antibodies to lose their efficacy by unproductive protein-protein association, which is likely triggered by the local unfolding of certain critical parts of the IgG structure. In this project we will develop a new sensor based on the Hsp70 chaperone with functionality that enable monitoring the generation of the aggregation-prone states of IgG and its fragments.
Principal Investigator: RNDr. Gabriel Žoldák, PhD.
Period: 2019–2023
Towards highly seletive cancer treatment: Endogenous lipoprotein-DARPin complexes as a new generation of targeted drug delivery vehicles (DARLINK)
Project objective: The ultimate goal of the project is to develop a new generation of drug vehicles (DARLINK(s)) with a high payload capacity showing a strong potential for high affinity binding to specific receptors on tumor cells. DARLINK can be tailored for mutated cancer cell receptors of individual patients and thus contribute to personalized treatment of cancer.
Principal Investigator: prof. RNDr. Pavol Miškovský, DrSc.
Period: 2016–2020
Conversion of integral membrane protein into water soluble form: the case of GPCR
Project objective: The principal goal of this project is to provide „proof of principle“ about possibility to transform of integral membrane protein into its water-soluble analogue. Successful reaching of this goal will provide information and tools for the modification of solubility also others, not only membrane, proteins.
Principal Investigator: doc. RNDr. Erik Sedlák, PhD.
Period: 2016–2020
Final evaluation: excellent results
Specialised Laboratory for Teaching and Advancing Protein Crystallography in a Virtual Reality Environment
The primary objective of this project is to establish effective infrastructure for a teaching laboratory that will provide the materials, hardware and software required for practical training and the advancement of protein crystallography at UPJŠ. The purpose of the laboratory will be to provide students with a supportive interdisciplinary environment in which they can acquire and deepen their knowledge and practical skills in protein research using molecular biology and biochemical techniques, as well as modern interactive technologies such as VR.
Principal Investigator: UPJŠ, RNDr. Michal Nemergut, PhD.
Period: 1/2024 – 12/2026
KEGA eduLab – A Teaching Laboratory for Lab-on-a-Chip Technology to Accelerate Innovation in Diagnostic Methods in Slovakia (005UPJŠ-4/2021)
The current pandemic situation has radically defined new, specific requirements for teaching the conceptual development of diagnostic tools intended to protect public health. The development of modern diagnostic methods requires an interdisciplinary approach combining biology with theoretical and experimental physics, which is currently lacking in the academic environment. The project aims to provide an innovative environment for teaching lab-on-a-chip (LoC) technology that encompasses all key stages of development. Students will progressively explore the basic principles of microfluidic devices and their physical modelling, construct their own lab-on-a-chip devices capable of laser-based optical manipulation of microparticles, and evaluate the measured data. The laboratory tools and equipment will enable students to acquire the practical and theoretical skills needed to master modern lab-on-a-chip technologies, with the potential to develop their own applications, for example in biomedical diagnostics.
Principal Investigator: UPJŠ, doc. RNDr. Gabriel Žoldák, PhD.
Period: 01/2021 – 12/2023
Heme Protein in Action: Novel Insights into it’s Biology From Theory and Experiments
Project objectives: Heme-proteins are an important class of proteins carrying out several key processes of life. The heme-iron atom in heme-proteins shows astrong binding preference to some ligands which are root causes of clinical complexities such as CO poisoning & hypoxia. We aim toelucidate the mechanistic details, resolved in time, of the ligand-binding process in heme-protein using ultrafast X-ray techniques.
Principal investigator: Dr. Krishna Khakurel Institute of Physics ASCR, ELI beamlines, Za Radnicí 835, Dolní Břežany, 252 41 , CZ, Slovakia partner: UPJŠ, doc. RNDr. Gabriel Žoldák, DrSc.
Period: 02/2023 – 06/2024
Euro-BioImaging je rozsiahly celoeurópsky projekt výskumnej infraštruktúry zaradený do cestovnej mapy Európskeho strategického fóra pre výskumné infraštruktúry (ESFRI). Prípravná fáza projektu trvala od decembra 2010 do mája 2014 a bola financovaná Európskou komisiou. Euro-BioImaging sa v súčasnosti nachádza v prechodnej fáze, počas ktorej zástupcovia 12 krajín a EMBL ako medzinárodnej organizácie spolupracujú na realizácii tejto infraštruktúry.