Current projects
KEGA
Špecializované laboratórium pre výučbu a rozvoj proteínovej kryštalografie v prostredí virtuálnej reality
Primárnym cieľom tohto projektu je vytvoriť efektívnu infraštruktúru pre edukačné laboratórium, ktoré bude poskytovať materiálové, hardvérové a softvérové prostriedky pre praktickú výučbu a rozvoj proteínovej kryštalografie na UPJŠ. Účelom tohto laboratória bude poskytnúť študentom priaznivé interdisciplinárne prostredie, ktoré umožní získať a prehĺbiť si vedomosti a praktické zručnosti v oblasti výskumu proteínov využívajúc molekulárno-biologické a biochemické postupy, ako aj moderné interaktívne technológie, ako napríklad VR.
Hlavný riešiteľ: UPJŠ, RNDr. Michal Nemergut, PhD.
Doba trvania projektu: 1/2024 – 12/2026
Openmed
Open Scientific Community for Modern Interdisciplinary Research in Medicine (OPENMED)
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
BioPickmol
Vývoj nanosenzorických fotonických systémov na rýchlu detekciu vírusov využitím metód riadenej evolúcie proteínovýchplatforiem: prípad SARS-CoV-2
Funkcionalizácia povrchu čipu nanovrstvou molekúl špecifických proteínov vyvinutých metódou riadenej evolúcie vybraných proteínových platforiem. Tvorba nanovrstiev proteínov na detekčnom čipe bude prebiehať pomocou kontrolovanej špecifickej chemickej konjugácie, čim dosiahneme optimálnu efektivitu viazania a reprodukovateľnosť detekčných vlastností. Po nanesení vzorky inaktivovaného vírusu na funkcionalizovaný čip bude prítomnosť vírusu detegovaná na základe zosilneného ramanovského spektra povrchovými plazmónmi. Na detekciu signálu z funkcionalizovaných čipov bude vyvinutý detekčný systém bioRAMASCOPE. bioRAMASCOPE bude spĺňať špecifické požiadavky týkajúce sa detekčných limitov a spoľahlivosti prevádzky vyžadovaných pre detekciu vírusu SARS-CoV-2. Pomocou moderných selekčných metód proteínového inžinierstva sa budú vyvíjať artificiálne proteíny ako nové biologické entity s väzobnou funkciou, ktorá sa špecializuje na špecifické viazanie inaktivovaných vírusov. Na základe kombinácie viazania rôznych epitopov plánujeme dosiahnúť vysokú citlivosť a špecificitu vyselektovaných proteínových platforiem voči rôznym typom vírusov, vrátane SARS-CoV-2.
Hlavný riešiteľ: UPJŠ, doc. RNDr. Gabriel Žoldák, PhD.
Doba trvania projektu: 01/2021 – 06/2023
KEGA eduLab
KEGA eduLab – edukačné laboratórium lab-ona-chip technológie pre zrýchlenie inovácií diagnostických metód na Slovensku (005UPJŠ-4/2021)
Súčasná pandemická situácia radikálnym spôsobom zadefinovala nové špecifické požiadavky na výuku koncepčného vývoja diagnostických nástrojov s úlohou ochrany zdravia spoločnosti. Vývoj moderných diagnostických metód vyžaduje kombináciu biologického a teoreticko-experimentálneho fyzikálneho interdisciplinárneho prístupu, ktorý momentálne absentuje v akademickom prostredí.Cieľom projektu je poskytnúť inovatívne prostredie na výučbu lab-on-a-chip technológie (LoC),ktorá zahŕňa všetky dôležité štádia vývoja. Študenti sa budú postupne venovať základným princípom mikrofluidných zariadení a ich fyzikálnemu modelovaniu, skonštruujú vlastné lab-on-a-chip zariadenia so schopnosťou laserovej optickej manipulácie mikročastíc a vyhodnocovaním nameraných dát. Nástroje a zariadenie laboratória umožnia študentom získať praktické a teoretické zručnosti pre komplexné zvládnutie moderných lab-on-a-chip technológií s potenciálnou možnosťou pre vývoj vlastných aplikácií, napr. v oblasti diagnostiky v biomedicíne.
Hlavný riešiteľ: UPJŠ, doc. RNDr. Gabriel Žoldák, PhD.
Doba trvania projektu: 01/2021 – 12/2023
VEGA
Vývoj a optimalizácia bakteriálneho expresného systému patologických foriem ľudského ľahkého reťazca imunoglobulínu IgG (VEGA 1/0024/22)
Bakteriálna produkcia rekombinantých proteínov zohráva dôležitú úlohu v základnom výskume pochopenia molekulovej podstaty patologických foriem ľudských proteínov. Okrem výskumu sú tieto rekombinantné proteíny potrebné pre efektívny vývoj diagnostických platforiem. Existencia veľkého množstva vhodných expresných vektorov ako aj jednoduchá kultivácia baktérií E. coli umožňuje škálovateľnú produkciu proteínov. V tomto projekte sa v prvom kroku zameriame na optimalizáciu expresie verejne dostupných patologických foriem ľahkého reťazca imunoglobulínu G v E. coli. V druhom kroku pripravíme pomocou techník molekulovej biológie nové tandemové proteínové konštrukty obsahujúce patologicky ľahký reťazec, ktorý je kovalentne spojený s proteínom patriacim do skupiny tzv. solubility enhancer tag. Štúdiom vplyvu 5 rôznych druhov solubility enhancerov (SUMO, MBP, SlyD, GB1 a GST) na rozsah expresie ľahkého reťazca získame optimálny bakteriálny expresný systém.
Hlavný riešiteľ : UPJŠ, doc. RNDr. Gabriel Žoldák, DrSc.
Doba trvania projektu: 01/2022 – 12/2024
Visegrad Funds
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
VEGA
Study and modification of properties of spider protein overexpressed in Escherichia coli
Modification of catalytic properties of haloalkane dehalogenases by protein evolution methods
APVV
Period: 2021–2025
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.
VEGA
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
APVV
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
Completed projects
VEGA
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
APVV
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
APVV
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
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.
EuroBioImaging
Euro‐BioImaging is a large‐scale pan‐European research infrastructure project on the European Strategy Forum on Research Infrastructures (ESFRI) Roadmap. Preparatory Phase of the project lasted from Dec 2010 to May 2014 and was funded by the EC. Euro-BioImaging is now in the interim phase, with representatives of 12 countries and EMBL as international organisation working together towards the implementation of the infrastructure.