head of the group:
associate professors:
doc. Ing. Jaroslav Zelenka, Ph.D.
assistant professors:
Ing. Markéta Častorálová, PhD.
Ing. Eva Jablonská, Ph.D.
Ing. Vladimíra Pavlíčková, Ph.D.
Ing. Nikola Vrzáčková, Ph.D.
technician:
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Technická 5
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Also available at Zenodo
Department of biochemistry and microbiology focus on basic research in areas of retroviral molecular biology, proteomics, plant physiology and molecular genetics, enzymology, environmental microbiology, food microbiology and bioanalytical methods. These activities create a platform for applied research aimed at developing modern therapeutic approaches, bioremediation of inorganic and organic pollutants, monitoring food safety and quality (the department also operates accredited Testing Laboratory of the Institute of Biochemistry and Microbiology) or plant-pathogen interaction. Research in our department is in many cases interdisciplinary and, in addition to close professional cooperation between the individual laboratories of the department, it would be unthinkable without cooperation with a number of national and foreign groups within the framework of joint research programs and projects. Currently, we are working on projects supported by the Czech Science Foundation, Technology Agency of the Czech Republic, Ministry of Agriculture of the Czech Republic, Ministry of Industry and Trade of the Czech Republic and the Ministry of Education and Sports.
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Advanced Biochemistry, Applied Enzymology, Environmental Microbiology, Food microbiology and Genetic engineering are delivered in English for foreign students.
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1) Virology
In the field of virology, which deals with the study of the structure and biology of viruses and their pathogenesis, we focus mainly on retroviruses and, more recently, in cooperation, also on flaviviruses. Both Retrovirideae and Flaviviridae are enveloped RNA viruses. The aim of our research is to clarify selected steps in the life cycle of viruses, focusing mainly on the late phase of viral infection. Understanding the molecular nature of these steps might open the possibility of developing new types of drugs. Using molecular biological methods, we study the structure of viral proteins, the functional significance of their structural domains, their mutual interactions, interactions with RNA and membranes and the transport of viral proteins and whole particles in an infected cell. We also study the structure and mechanism of formation of mature and immature retroviral particles.
2) Medicinal chemistry: Theranostics and multimodal therapy
Natural products are the basis of clinical therapy for cancer and other diseases. Their therapeutic effects can be modified with chemical derivatization in order to reduce unwanted side effects, increase cytotoxicity and selectivity towards pathological cells, change their mechanism of action, etc. In our research group, we mainly focus on basic research of toxicity and mechanism of action of novel antimitotic derivatives (e.g., colchicine and paclitaxel), inhibitors of sarco-/endoplasmic reticular Ca2+-ATPase (e.g., thapsigargin and trilobolide) and cardiac glycosides (e.g., digitoxin and digoxin). Most of the derivatives we study are developed with the aim to be utilized in multimodal and combination therapy as well as theranostics of cancer. Theranostics is based on diagnostic and therapeutic properties combined in one molecule, which often consists of a natural product conjugated to a fluorescent moiety.
3) Cytocompatible and antimicrobial materials for research and medicinal applications
Another research topic addressed by our scientific group is the study of tailor-made polymers and metallic materials for medical applications for soft and hard tissue replacements, but also for research purposes (e.g., single cell cultivation and analysis). The aim of this research is to develop novel possibilities for functional replacement of damaged tissues but also to understand the basic mechanisms of cell-cell and cell-material interactions in dependence on its nano- and microstructured topology. We focus on evaluation of material cytocompatibility, cytotoxicity and antibacterial properties using cell biological and microbiological methods. Moreover, methods of molecular biology are utilized to study the mechanism of cell adhesion, interaction of cells with materials at the molecular level, and cell differentiation.
4) Photodynamic therapy and molecules for photoimaging
Photodynamic therapy is a non-invasive therapy using special molecules that, when activated by light, produce highly reactive oxygen species applicable for the eradication of tumors, microorganisms, or the treatment of skin diseases. We collaborate on the development of advanced photoactive molecules and study the molecular mechanisms of their action and localization in living tumor cells in real time. We focus on these aspects in the study of the effectiveness of photoactive molecules including both inorganic materials (e.g., molybdenum clusters) and organic molecules (e.g., porphyrins, phthalocyanines, halogenated BODIPY). In addition, we focus on the development of novel fluorescent probes for imaging techniques, which are an indispensable tool for medicine and molecular biological research. Fluorescence probes allow us not only to visualize and study different cellular structures, but also to reveal the molecular basis of various diseases. Our goal is to eliminate the limitations of available probes, such as high toxicity, low specificity or insufficient photophysical properties. We use both common and highly specialized fluorescence microscopy methods (SIM, PALM / STORM) to evaluate these probes.
5) Biologically active substances
We study the properties of plant extracts or isolated compounds with a focus on both beneficial effects and possible negative effects. Our goal is to identify biologically active substances and characterize their beneficial effects while excluding possible toxicological effects. Special emphasis is placed on biologically active substances with the ability to modulate multiple drug resistance.
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Metallic materials for orthopaedic applications
When developing novel biomaterials for orthopaedic applications, the goals to reach are: suitable mechanical properties, antibacterial effect and the ability of material to accelerate healing. Another direction is the development of degradable metallic materials for temporary applications, which would mean no need of reoperation. Novel biomaterials developed by our co-operators must be first tested and approved. Our group deals with first stage of biomaterials testing using cell cultures and relevant methods..
Human immortalized stem cells derived from adipose tissue grown on a titanium alloy with nanotubular surface modification (nuclei in blue, actin filament in red); Electron-microscopic image of murine fibroblasts grown on degradable magnesium alloy (magnification 2000 x)
The methods we use
We determine corrosion rate in biological media under physiological conditions, we test in vitro cytotoxicity of biomaterials according to ISO 10993-5 (elution test followed by determination of metabolic activity by resazurin assay) and we examine colonisation of material’s surfaces using microscopic techniques (using fluorescence as well as scanning electron microscopy). We use murine fibroblasts and cell lines derived from human bone tissue as cell models. We also test antibacterial properties of the biomaterials.
Contact
Ing. Eva Jablonská, Ph.D.
doc. Ing. Jan Lipov, Ph.D.
prof. Ing. Tomáš Ruml, CSc.
Publications
Cooperation
- The Department of Metals and Corrosion Engineering , UCT Prague
- The Department of Glass and Ceramics , UCT Prague
- Department of Physics of Materials, Faculty of Mathematics and Physics, Charles University
- The Institute of Physics, ASCR
REDOX Lab
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We are a friendly and open laboratory that focuses on the topics of oxidative stress, antioxidants and redox signalling in fields related to human health. We research in microbiology, cell biology, biochemistry, chemical biology and materials science.
What is our goal?
We are engaged in a mixture of basic and applied research to understand the mechanisms of various diseases and then to find new smart approaches to prevent and treat them. We collaborate with experts in other departments, including physicists, chemists, materials scientists, physiologists and physicians.
What can you find here?
We'll keep you up to date on the exciting things we're up to - our latest projects, findings and maybe even behind the scenes. But it's not just about our work in the lab. We also share a lot of our knowledge. You'll find educational materials, fun facts and some tips for budding scientists on our sites. We're all about spreading the love of science far and wide.
So bookmark this page, follow us on social media and join us on this wild ride through a fascinating world of 
. If you've got questions or just want to say hi, drop us a line - we'd love to hear from you.
WE ARE DEALING WITH
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Head of the lab
assoc. prof. Ing. Jaroslav Zelenka, Ph.D. 
Postdoc
PhD students
Master's students
Bc. Denisa Pineckerová
Bc. Roman Skala
Bc. Tereza Najmanová
Bc. Anna Krátká
Bc. Tereza Vernerová
Bc. Viktorie Svadbová
Bachelor's students
Kateřina Pavličíková
Jiří Zvoníček
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The molecular clusters based on Mo6I8 core with variable outer ligands are capable to generate of highly reactive singlet oxygen upon illumination with light or irradiation with X-rays. Reactive oxygen species, such as singlet oxygen, react with biopolymers such as proteins, DNA, and lipids. Unreparable damage of intracellular components can cause various types of cell death.
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The Mo6 compounds are prepared at the Institute of Inorganic Chemistry, Czech Academy of Sciences by Dr. Kamil Lang and Dr. Kaplan Kirakci.
We culture normal and cancer cells of human origin and illuminate them with special light sources or with X-rays. Our hypoxic chamber allows us to work under low physiologically relevant levels of oxygen. We can determine the cellular uptake and localization of cluster compounds or nanoparticles with a confocal microscope or with a structure illumination super-resolution microscope (SIM). The nanoparticles are also specifically targeted to cancer cells using molecular recognition.
The promising materials are further tested on in vivo mouse models in collaboration with Dr. Milan Reiniš from the Institute of Molecular Genetics, Czech Academy of Sciences.
The antibacterial properties of compounds, layers, and particles are determined using model strains of bacteria relevant in clinics. The bacteria are cultured in the form of biofilm, a naturally occurring multicellular structure with enhanced physical and chemical resistance.
The Microbiology Division focuses on various microbiology topics surrounding metabolism, oxidative stress, and research for new antimicrobial compounds. Redox laboratory is dedicated to exploring the intricate mechanisms by which light, oxidative stress, and other environmental factors impact microorganisms at the cellular and molecular levels. We work with either common bacterial species or yeasts.
[ikona] => [obrazek] => [ogobrazek] => [pozadi] => 0004~~881MLspPyszPyU-vVEjLzEvMAQA.png [obsah] =>Photodynamic inactivation of bacteria (PDI)
We investigate the fascinating world of photoinactivation, a process based on the same principle as photodynamic therapy by which bacteria are rendered nonviable by reactive oxygen species (ROS), generated by photosensitizers exposed to specific wavelengths of light. By delving into the intricacies of this phenomenon, we aim to develop novel methods for disinfection and sterilization, potentially revolutionizing fields such as healthcare, food safety, and water treatment.
We test novel antibacterial compounds, such as molybdenum clusters, and other photosenzitizers for PDI such as well-researched methylene blue or nanorobots. We evaluate toxic effects against planktonic forms of bacteria or more resistant, commonly occurring biofilm forms.
Oxidative stress in microorganisms
Additionally, the division places a significant emphasis on oxidative stress in bacteria and yeasts. Oxidative stress occurs when cells are subjected to an imbalance between reactive oxygen species (ROS) production and their detoxification mechanisms. We seek to unravel how microorganisms and yeasts respond to oxidative stress and adapt to their environments. This research is vital in understanding the virulence and survival strategies of pathogenic microorganisms, as well as the role of yeasts in various biotechnological processes.
We use various techniques of cultivation, antioxidant capacity assays, ROS generation detection using different fluorescent probes, optical microscopy, confocal fluorescent microscopy, and more.
We are dedicated to investigating the immunotoxicity and toxicity of new materials and pollutants and their impact on cells, with a particular focus on macrophages and basophils. We are deeply committed to advancing our understanding of the interactions between these materials and the human immune system, specifically in relation to the generation of reactive oxygen species (ROS) and the development of allergies. Understanding how these materials affect our cells is critical for assessing their safety in industrial and medical applications.
Macrophages are one of the key players in the immune response, and we investigate how exposure to novel materials can influence their function. We study the phagocytic activity, cytokine production, and ROS generation in human macrophages when exposed to different materials to determine their impact on immune defense mechanisms.
Other immune cells basophils are essential in allergic reactions, and we explore how exposure to novel materials can trigger allergic responses. Our research focuses on the degranulation of basophils and the release of pro-inflammatory mediators, which play a pivotal role in allergy development, which nowadays become more common than ever before.
Reactive oxygen species are involved in various cellular processes, including immune responses. We investigate how new materials can induce ROS production in immune cells, and evaluate the potential consequences of elevated ROS levels, such as oxidative stress and inflammation.
We are dedicated to advancing the field of immunotoxicology and its applications in assessing the safety of emerging materials. By investigating the impact of novel materials on human immune cells, as well as the impact of elevated ROS and allergy development, we aim to provide critical insights that promote the responsible and safe use of these materials in various industries while safeguarding human health.
Lactate, or lactic acid anion, is a relatively large and long-standing topic in our laboratory. We have all probably heard the term in relation to the human body at some point, most often in connection with physical exhaustion. Indeed, for a long time, lactate was viewed only as a waste product of anaerobic glycolysis when there is an inadequate supply of oxygen to the tissues, which is responsible for muscle pain and fatigue. However, nothing is black and white, and recent research has partially contradicted these findings while showing that it can also be beneficial to the body, as it is also an important signalling molecule involved in several metabolic processes or a non-negligible energy source for our nerve cells.
So how's the whole lactate thing going? Generally speaking, lactate can have both a positive and negative role in the context of the human body. In particular, lactate produced by tumour and ischemic tissue has adverse effects. On the other hand, positive effects have been observed for lactate produced during physical exertion or consumed as a functional component (postbiotic) of fermented foods, including, for example, adaptation of the body to stress conditions through mitochondrial hormesis, faster tissue regeneration and, in turn, delayed ageing, or control of adipose tissue homeostasis and reduced risk of obesity and insulin resistance.
In our laboratory, we are working on several projects focusing mainly on lactate and its health benefits. For example, we are looking at the effects of lactate at the cellular level in human fibroblast tissue lines. We interact with lactate over a long period of time to simulate the situation that occurs in the body during and after intense exercise and try to detect any physiological changes in these cells. In particular, we focus on differences in growth rate and the transition to senescence. We also look at effects on cellular antioxidant mechanisms and mitochondrial activity or potential protection against carcinogenesis. However, we are not limited to single cells and tissue lines, our laboratory is also involved in investigating the effects of lactate in mouse models that have been supplemented with lactate in their diet. We are currently working on analysing their gut microbiome and liver proteome to discover either positive or negative changes that could be related to the presence of lactate in the diet. Ideally, we could thus get an answer to the question of what is the essence of the benefits of eating fermented foods, or theoretically contribute to the development of a lactate-based drug that would target the alleviation of civilisation diseases, which is and unfortunately will undoubtedly be even more of a problem in the human population in the future.
Treatment of cardiovascular, neurodegenerative and autoimmune diseases, repair of damaged tissues, anti-cancer therapy, mitigation of obesity-related risks, including the development of metabolic syndrome and type 2 diabetes, and increased sports performance, faster recovery after strenuous training or higher yields in agriculture. All these words and phrases have one common link, namely molecular hydrogen.
Yes, hydrogen! The smallest, simplest and most abundant element in the universe, it is most often talked about in the scientific community as the fuel of the future or in connection with nuclear fusion. In contrast, it has not received much attention in the biological and biochemical fields and has been considered an inert molecule with minimal effects on living organisms. A breakthrough came in 2007 when specific antioxidant effects were discovered in tissue lines. Intensive research has also begun in these scientific fields, and dozens and hundreds of scientific articles have been published attributing antioxidant, antiapoptotic and anti-inflammatory effects to molecular hydrogen, which can be used in the prevention and treatment of many diseases. It has also been found to have a positive effect on mitochondrial function and may be involved in several signalling pathways in cells. However, its exact mechanism of action has not yet been described and many related things are still waiting to be discovered.
The study of the biological effects of molecular hydrogen is a relatively new topic in our laboratory, on which we are collaborating with Associate Professor Michal Botek, PhD from the Faculty of Physical Education of Palacký University in Olomouc. While proffesor Botek administers molecular hydrogen in the form of hydrogenated water directly to athletes, in whom he observes, for example, an increase in their performance under given conditions, in our laboratory, we focus on the study of the effect of water enriched with molecular hydrogen on human tissue cultures, in which we try to detect possible changes in cell physiology and metabolism. Currently, we are particularly interested in the effect on cellular levels of reactive oxygen species (ROS), the overall cellular antioxidant capacity or the expression of the transcription factor Nrf2, which is mainly responsible for increasing the activity of antioxidant mechanisms in cells.
Chlorinated paraffins
The contaminants pose a significant risk to the environment and human health. Among a relatively new and underexplored class of contaminants are chlorinated paraffins, which have replaced the high-risk polychlorinated biphenyls in many industry sectors.
Chlorinated paraffins are polychlorinated n-alkanes formed by radical chlorination initiated by UV light. According to the length of the carbon chain, they can be divided into short SCCP, medium MCCP, and long LCCP. SCCPs have been used in industry as flame retardants, metalworking fluids, and paints or sealant components. In 2017, however, SCCPs were classified as persistent organic pollutants under the Stockholm Convention. Their production and use are, therefore, restricted and regulated. However, as is common in the industry, after the prohibition of SCCPs, the market has shifted to a novel group of compounds, MCCPs, which have very similar properties, and therefore we expect similar environmental effects. The production of MCCPs is rising annually, potentially leading to severe ecological contamination that could take decades to remediate.
Like other organochlorine compounds, chlorinated paraffins are non-polar substances readily accumulating in fatty tissues. An important question regarding the in vitro action of CPs is whether CPs can penetrate the cell or affect cell physiology as extracellular agents. The answer to this question still needs to be clarified. On the other hand, SCCPs have been found to cause indirect and direct toxicity. In addition to in vitro cellular models, chlorinated paraffins have been studied using animal models ranging from snakes and frogs to chickens and various other birds to laboratory mice and rats. Significant accumulation of SCCPs and MCCPs was observed in all organisms under investigation.
CPs have also been found in biological matrices such as plasma, placenta, umbilical cord blood and breast milk. Both SCCPs and MCCPs have been shown to cross the placenta into the fetus and subsequently into the body of newborns through breastfeeding. Data from biomonitoring studies on the presence of CP in human tissues are limited, as most CP studies focus only on China, the largest producer and consumer of CP.
Any further knowledge in the field of chlorinated paraffins may lead to the determination of their effects on living organisms and potentially restricting or banning their use in industry.
prof. Ing. Tomáš Ruml, CSc.
Tel: +420 220443022
Email: tomas.ruml@vscht.cz
EDUCATION
| 1984 | PhD. in Biological Sciences at the Prague Institute of Chemical Technology (Study of thiamine excretion in mutants of Saccharomyces cerevisiae) |
| 1973–1978 | M.S. Institute of Chemical Technology, Prague (Dept. Fermentation Technology and Bioengineering, diploma thesis: Physiological characteristics of Candida utilis growing on ethanol) |
WORK EXPERIENCE
| 09/2013-08/2020 | Head of the Department of Biochemistry and Microbiology, UCT, Prague |
| 01/2012–12/2019 | Dean of the Faculty of Food and Biochemical Technology; UCT, Prague |
| 2009/2011 | Vice rector for International affairs, UCT, Prague |
| 2006/2009 | Vice rector for R&D, Faculty of Food and Biochemical Technology; UCT, Prague |
| 2002 | professor, Department of Biochemistry and Microbiology, UCT, Prague |
| 01/1996 – dosud | associated professor, Department of Biochemistry and Microbiology, UCT, Prague |
| 09/1984 | assistant, Department of Biochemistry and Microbiology, UCT, Prague |
FOREIGN STUDY STAYS
University of Alabama at Birmingham - virology (two years: 1989-1991), 1994 (3 months), 1996 (3 months), 1998 (3 months); City College New York 1993 (3 months)
ORGANIZATIONAL ACTIVITIES
Main organizer of world Retrovirus Assembly Meetings: 14.-18. October 2000, 2.-6. October 2004 and 4.-8. October 2008 in Prague, co-organizer of two The FEBS Congresses, and 5 other congresses.
MAJOR RESEARCH ACTIVITES
Structures, interactions, targeting and assembly of retroviral proteins. Developed a fundamental method for in vitro assembly of retroviral particles, which represents a basic technology used in numerous prestigious laboratories worldwide.
Activity of molecules and nanoparticles for photodynamic therapy.
Biological effects of molecules and materials on human cells.
Bioprospection – analysis of medicically beneficial effects of marine and plant resources.
PUBLISHING ACTIVITY
Scientific papers in WoS: 206
Number of citations without self-citations: 3 343
H-index: 31, Co-author of 8 patents (two of which were realized by a license agreement)
PEDAGOGICAL ACTIVITY
Established new study program – Forensic analysis, initiated and co-established a new study program Bioinformatics.
Introduced and taught new university lecture courses: Molecular genetics, Genetic engineering, Genetic manipulations - laboratory course, Industrial microbiology; Taught: Microbiology. Laboratory: Microbiology, Biochemistry, Microbial analysis of foods.
Supervised 84 defended diploma works (4 awarded by J. Hlávka Prize for the best diploma thesis) and 24 Ph.D. students successfully defended their theses (one 3rd place in Sanofi Pasteur prize, two awarded by Votoček stipend and one by J. Hlávka Prize).
AWARDS
| 2012 | of Minister of Education, Youth and Sports: “For extraordinary results in research”; |
| 2014 | of rector UCT Prague: “For outstanding research and successful promotion of science”; |
| 2015 | Award of Vietnamese president "For significant contribution to understanding between nations" |
Home Publications
Photobiology of materials based on Mo6I8 clusters and porphyrin frameworks
The molecular clusters based on Mo6I8 core with variable outer ligands and the porphyrin frameworks share the ability to catalyze the production of highly reactive singlet oxygen upon illumination with light or irradiation with X-rays. They serve for the preparation of soluble molecules, nanolayers, or nanoparticles that could kill cancer cells or pathogenic bacteria upon illumination or irradiation. In collaboration with Dr. Kamilem Langem a Dr. Kaplanem Kirakci from the Institute of Inorganic Chemistry, Czech Academy of Sciences, our group test the biological properties of such novel materials. We culture normal and cancer cells of human origin in our tissue culture facility and illuminate them with special light sources or with X-rays. Our hypoxic chamber allows us to work under low physiologically relevant level of oxygen. We can determine the cellular uptake and localization of cluster compounds or nanoparticles with confocal microscope or with structure illumination super-resolution microscope (SIM). The nanoparticles are also specifically targeted to cancer cells using molecular recognition. The promising materials are further tested on mouse models in collaboration with Dr. Milanem Reinišem from Institute of Molecular Genetics, Czech Academy of Sciences. The antibacterial properties of compounds, layers and particles are determined using our microbiology facility and model strains of bacteria relevant in clinics. The bacteria are cultured in the form of biofilm, a naturally occurring multicellular structure with enhanced physical and chemical resistance.
Funding
- Biomaterials based on octahedral molybdenum clusters as singlet oxygen radiosensitizers, GA18-05076S, Czech Science Fundation
Publications
- Kirakci K., Nguyen T.K.N., Grasset F., Uchikoshi T., Zelenka J., Kubát P., Ruml T., Lang K.: Electrophoretically Deposited Layers of Octahedral Molybdenum Cluster Complexes: A Promising Coating for Mitigation of Pathogenic Bacterial Biofilms under Blue Light. ACS Appl Mater Interfaces, 2020. IF 8,758
- Kirakci K., Demel J., Hynek J., Zelenka J., Rumlová M., Ruml T., Lang K..: Phosphinate Apical Ligands: A Route to a Water-Stable Octahedral Molybdenum Cluster Complex. Inorg Chem 58:16546–16552, 2019. IF 4,850
- Kirakci K., Zelenka J., Rumlová M., Cvačka J., Ruml T., Lang K.: Cationic octahedral molybdenum cluster complexes functionalized with mitochondria-targeting ligands: photodynamic anticancer and antibacterial activities. Biomater Sci 7:1386-1392, 2019. IF 5,831
- Kirakci K., Zelenka J., Rumlová M., Martinčík J., Nikl M., Ruml T., Lang K.: Octahedral molybdenum clusters as radiosensitizers for X-ray induced photodynamic therapy. J Mater Chem B 6:4301-4307, 2018. IF 5,047
- Hynek J., Zelenka J., Rathouský J., Kubát P., Ruml T., Demel J., Lang K.: Designing Porphyrinic Covalent Organic Frameworks for the Photodynamic Inactivation of Bacteria. ACS Appl Mater Interfaces 10:8527-8535, 2018. IF 8,456
- Buzek D., Zelenka J., Ulbrich P., Ruml T., Krizova I., Lang J., Kubat P., Demel J., Kirakci K., Lang K.: Nanoscaled porphyrinic metal-organic frameworks: photosensitizer delivery systems for photodynamic therapy. J Mater Chem B 5:1815-1821, 2017. IF 5,047
head of the group:
associate professors:
doc. Ing. Jaroslav Zelenka, Ph.D.
assistant professors:
Ing. Markéta Častorálová, PhD.
Ing. Eva Jablonská, Ph.D.
Ing. Vladimíra Pavlíčková, Ph.D.
Ing. Nikola Vrzáčková, Ph.D.
technician:
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