Dissertation topics for PhD. study programmes for the academic year 2026/2027
Pavol Jozef Šafárik University in Košice, Faculty of Science
Institute of Biology and Ecology
Plant physiology (FRd)
Title
Ecophysiological differentiation of selected taxa of the genera Leontodon and Scorzoneroides
Language
SK
Abstract
The genera Leontodon and Scorzoneroides (Asteraceae) represent an important group of meadow and pasture species and exhibit a broad ecological amplitude. Despite their distribution in Central Europe, knowledge of their ecophysiological adaptations, responses to environmental gradients, and mechanisms of ecological differentiation remains fragmentary. A better understanding of these processes may clarify the evolutionary dynamics of the group, the mechanisms of specialization, and the potential of species to respond to changing climatic conditions. The aim of the thesis will be to comprehensively analyse the ecophysiological differentiation of selected taxa in Central Europe and to identify the key mechanisms that enable their ecological diversification and adaptation to various environments, as well as to update the taxonomic and evolutionary understanding of the group. The research will focus primarily on morphological, anatomical, and karyological characteristics, as well as on the assessment of genome size variation and the specialization of taxa in their natural habitats. The results may be applied in biodiversity conservation, grassland ecosystem management, and in predicting the responses of plant communities to climate change.
Objective
1. The first aim of the thesis is to comprehensively analyze the ecophysiological differentiation of selected taxa of the genera Leontodon and Scorzoneroides in Central Europe and to identify the key mechanisms that enable their ecological diversification and adaptation to different environments.
2. The second aim of the thesis is to update the taxonomic and evolutionary knowledge of selected species of the genus within the family Asteraceae.
References
Samuel R., Gutermann W., Stuessy T. F., Ruas C. F., Lack H.-W., Tremetsberger K., Talavera S., Hermanowski B., Ehrendorfer F.: Molecular phylogenetics reveals Leontodon (Asteraceae, Lactuceae) to be diphyletic. American Journal of Botany 93(8): 1193–1205. 2006.
Ingimundardóttir G. V. , Tyler T., Cronberg N., Hedrén M. Andersson S.: Dressed for the occasion! Ecotypic divergence, phenotypic plasticity and taxonomic value of capitulum characters of Scorzoneroides autumnalis (Asteraceae). Nordic Journal of Botany 2024: e04211.
Tutor
prof. RNDr. Pavol Mártonfi, PhD.
Consultant
RNDr. Lenka Mártonfiová, PhD.
Title
Conservation physiology of selected rare and threatened bryophytes from extreme environment.
Language
SK
Abstract
Bryophytes are non-vascular plants that lack true roots and depend on water for reproduction. In ecosystem, they play a crucial role in moisture regulation, the prevention of soil erosion, and serve as pioneer organisms on bare surfaces. Due to their specialized ecological niches and lack of protective tissues, endangered bryophyte species are exceptionally sensitive to habitat loss and climate change. The protection of these species requires a combination of habitat restoration and the study of physiology and adaptive mechanisms, with a specific focus on laboratory cultivation to prevent their extinction.
The objective of this doctoral study is to examine bryophyte physiology and investigate the adaptive mechanisms and responses of endangered species to these environmental stressors. By integrating physiological profiling (such as chlorophyll fluorescence and oxidative stress markers) with environmental monitoring, the research aims to define the limits of their physiological plasticity. Furthermore, the project focuses on developing protocols for ex situ propagation including axenic cultures and fragmentation techniques to facilitate the restoration of these populations. Fluorescence microscopy can be utilized to visualize the activity of biochemical processes in bryophyte tissues responding to environmental stress. By employing specific fluorescence methods, we can monitor oxidative changes in real-time. An additional goal is the study of protective enzymatic reactions at the cellular level, providing high-resolution data on the physiological resilience of the target species. Ultimately, this work seeks to bridge the gap between laboratory physiological data and field-based conservation strategies, thereby providing a scientific foundation for the conservation of bryophytes in a changing climate.
Objective
The aim of the doctoral study is to examine the physiology of bryophytes and investigate the adaptive mechanisms and responses of endangered species to stress factors such as habitat loss and climate change.
Specifically:
1. By integrating physiological profiling (chlorophyll fluorescence, oxidative stress markers) with environmental monitoring, the research focuses on defining the limits of their physiological plasticity.
2. Development of protocols for ex situ propagation of endangered bryophyte species.
3. Study of protective enzymatic responses at the cellular level, providing high-resolution data on the physiological resilience of bryophyte species.
References
Scientific articles from databases Web of Science and Scopus.
Tutor
doc. RNDr. Michal Goga, PhD.
Consultant
prof. Dr. rer. nat. Marko Sabovljević, Dr. rer. nat.
Title
Plasticity of endoreplication in relation to genome size and ecophysiological factors.
Language
SK
Abstract
Genome multiplication, or endopolyploidization, represents the repeated doubling of the entire nuclear genome of a cell or only part of it and is one of the mechanisms of change in the ploidy level at the cellular level. It leads to the formation of polyploid cells and occurs during morphogenesis, i.e. differentiation of various organs of plants. The level of endopolyploidy is the result of the interaction of several factors, such as the systematic position of the plant species, the ploidy level, the genome size and the stage of plant development, the type of tissues and organs, and environmental conditions. Endopolyploidy is phylogenetically determined and is also common in economically important angiosperm families such as Fabaceae, Brassicaceae, Solanaceae or Orchidaceae. Previous studies have also often, but inconsistently, shown a negative relationship between endopolyploidy and genome size in plants. Especially significant are the previous studies of polyploids in the model species Arabidopsis thaliana conducted in the context of the ecophysiological differentiation of polyploids and the role of endopolyploidy in it. For a better understanding of the relationship between the extent of endopolyploidy and genome size, it is necessary to identify plant models where polyploidy does not contribute to genome enlargement. In this dissertation, the PhD candidate will aim to investigate the relationship between endopolyploidy and genome size and karyology, as well as the ecophysiologically conditioned modulation of endopolyploidy, using the examples of a little-studied group of plants from the family Boraginaceae (e.g., in the genera Pulmonaria and Onosma). One of the advantages of these taxa is the presence of species with high intracytotype variability in genome size (e.g., Onosma pseudoarenaria s.l. group), which will allow filtering out the effect of polyploidization in relation to endopolyploidy versus genome size. The applicant will have access to a wide range of promising research subjects where endopolyploidy has been partially studied. The applicant will learn various research methods, such as flow cytometry, DIC and fluorescence microscopy, histochemical methods, phenotyping of different organs and plant structures, or ecophysiological techniques.
Objective
In this dissertation, the PhD candidate will aim to investigate the relationship between endopolyploidy and genome size and karyology, as well as the ecophysiologically conditioned modulation of endopolyploidy, using the examples of a little-studied group of plants from the family Boraginaceae (e.g., in the genera Pulmonaria and Onosma).
References
Scientific articles from databases Web of Science and Scopus.
Tutor
doc. Mgr. Vladislav Kolarčik, PhD.
Title
Preference for isoflavonoid and flavonol formation under stress conditions in soybean.
Language
SK
Objective
The aim of the work is to evaluate the biosynthesis and accumulation of flavonoids and isoflavonoids under stress conditions using a model soybean variety (Glycine max), or other important cultivated varieties may be used for comparison. The substances will be analyzed by chromatography methods and identified by LC-MS. The biosynthesis of these substances will also be monitored at the level of expression of genes for biosynthetic reactions or transcription factors. The accumulation of genistein, daidzein, glycitein, formononetin, including the relevant glycosides and other substances will be monitored, as well as the influence of hormones (especially abscisic acid) on their production. The obtained results will be compared within the Fabaceae family with the aim of a deeper understanding of the regulation of the formation of isoflavonoids, which are typical for legumes.
References
scientific papers registered in WOS and/or SCOPUS
Tutor
doc. RNDr. Peter Paľove-Balang, PhD.
Title
Stres metabilites in Lotus sp. and their relevance in stress-response.
Language
SK
Objective
The aim of the work is the evaluation of the biosynthesis and accumulation of flavonoids and isoflavonoids under stress conditions (drought, UV-B or others) in the model species Lotus japonicus incl. its mutant lines. The influence of hormones and other regulatory substances will also be followed. The results will be compared in the forage-varieties of L. corniculatus, or in other species under the different external factors. Substances will be analysed by chromatographic methods and identified by LC-MS. The biosynthesis of these substances will also be monitored at the level of gene expression for biosynthetic enzymes or transcription factors. Tracking the accumulation of vestitol, clarifying its functions in plant defence. Other important isoflavonoids may be also focused.
References
scientific papers in journals registered in WOS and/or SCOPUS
Tutor
doc. RNDr. Peter Paľove-Balang, PhD.
Title
From extreme environments to industrial applications: Biotechnological potential of proteins and secondary metabolites from selected lichen species.
Language
SK
Abstract
Lichens represent one of the most important symbiotic relationships on earth. One reason is that they are pioneer organisms that colonize parts of the earth that are extremely inhospitable to higher plants. Together with mosses or cyanobacteria, they form small ecosystems that are directly involved in primary succession. The significance of lichens, however, extends beyond their ecological role. Survival in extreme conditions such as high UV radiation, frost stress or desiccation is enabled by the production of stress proteins. There is a lack of information about their biotechnological potential. In addition to these proteins, lichens also produce secondary metabolites, whose pharmaceutical potential is not negligible. However, the isolation of these unique substances is crucial and challenging.
The aim of the doctoral project is the systematic identification and characterization of proteins with high biotechnological potential encoded in the genomes of lichen symbioses. The work uses methods of comparative genomics and bioinformatics to search for unique biosynthetic gene clusters and enzymes involved in the metabolism of specific lichenophytes. Selected candidate genes will subsequently be subjected to cloning and heterologous expression, which will allow the production of functional proteins in laboratory conditions. Another goal will be the isolation and identification of secondary metabolites using Flash chromatography, the most efficient separation, the creation of protocols or derivatives of the obtained metabolites in order to increase their biological potential in the field of pharmacology.
The next phase of the research will focus on detailed biochemical and structural analysis of the obtained products with the aim of clarifying the relationship between their structure and catalytic properties. The project brings an innovative perspective on the use of the genetic wealth of lichens as a source of new biocatalysts for industrial biotransformation and pharmacology. The results of the work will contribute to the development of efficient procedures for the production of previously difficult-to-access natural substances under controlled conditions.
Objective
Scientific articles from databases Web of Science and Scopus.
References
The aim of the doctoral project is the systematic identification and characterization of proteins with high biotechnological potential encoded in the genomes of lichen symbioses. The work uses methods of comparative genomics and bioinformatics to search for unique biosynthetic gene clusters and enzymes involved in the metabolism of specific lichenophytes.
Tutor
doc. RNDr. Michal Goga, PhD.
Consultant
prof. RNDr. Erik Sedlák, DrSc.
Molecular Cytology and Genetics (MCGd)
Title
Biodiversity and bioprospecting of halophilic archaea from miocene salt deposits
Language
SK
Abstract
Bioprospecting of extreme environments provides clear evidence that extreme conditions naturally select microorganisms with modified biochemistry giving opportunity for new compounds, genes, and processes discoveries. The aim of the project is an in-depth exploration of the uncharted realm of halophilic archaea, focusing on the Miocene salt deposits as a unique and understudied environment. The Miocene salt deposits could serve as a natural repository of ancient genetic material, providing insights into the evolutionary history and ecological roles of halophilic archaea. By combination of advanced molecular techniques and culturing methods, an array of halophilic archaea from these deposits will be isolated and characterized. The bioprospecting potential of these halophilic archaea with applications in modern biotechnology, pharmaceuticals, and sustainable industries will be analyzed. Novel enzymes, biosurfactants, and bioactive compounds will be identified in addressing environmental challenges. The study will contribute significantly to the expanding knowledge of halophilic archaea ecosystems and highlights the protection and sustainable utilization of these microbial resources for future biotechnological advancements.
Objective
The aim of the work is to analyze the population of halophilic archaea from Miocene salt deposits using both cultivation and non-cultivation approaches.
References
McGenity, T.J.; Oren, A. Hypersaline Environments. In Life at Extremes:
Environments, Organisms and Strategies for Survival; Bell, E.M., Ed.; CAB
International: Oxfordshire, UK, 2012
Oren, A. Life in Hypersaline Environments. In Their World: A Diversity of
Microbial Environments, Advances in Environmental Microbiology; Hurst,
C.J., Ed.; Springer International Publishing: Cham, Switzerland, 2016
Ventosa, A.; Márquez, M.C.; Sánchez-Porro, C.; de la Haba, R.R. Taxonomy
of Halophilic Archaea and Bacteria. In Advances in Understanding the Biology
of Halophilic Microorganisms; Vreeland, R.H., Ed.; Springer: Dordrecht, The
Netherlands, 2012
Current scientific literature
Tutor
doc. RNDr. Peter Pristaš, CSc., univerzitný profesor
Consultant
RNDr. Lenka Maliničová, PhD.
Title
Ecogenetics and ecogenomics of extreme environments
Language
SK
Abstract
Ecogenetics and ecogenomics are emerging fields that explore the intricate relationships between genetic variation and environmental factors, particularly in extreme environments such as deep-sea vents, polar regions, and salt pans and springs. These extreme conditions exert unique selective pressures that shape the genetic architecture of organisms, driving adaptations at both the phenotypic and molecular levels. The aim of the project is to uncover the mechanisms of adaptation, resilience, and diversity among procaryotic extremophiles by integrating ecological and genomic data. The data obtained will not only enhance our understanding of microorganism’s biodiversity and evolutionary processes but also has should have implications for biotechnological applications, environmental conservation, and understanding potential life forms beyond Earth.
Objective
The aim of the project is to reveal the mechanisms of adaptation, resistance, and diversity among prokaryotic extremophiles by integrating ecological and genomic data. The result of the work will be linage of physicochemical characteristics of the environment with specific genetic and functional adaptations of prokaryotes, thereby contributing to a better understanding of the biodiversity of extreme ecosystems and their potential for biotechnological and environmental applications.
Tutor
RNDr. Jana Kisková, PhD.
Consultant
doc. RNDr. Peter Pristaš, CSc., univerzitný profesor
Title
Nanoparticle-induced biosynthesis of anthraquinones in plants of the genus Hypericum and their endophytic fungi
Language
SK
Abstract
Anthraquinones, including naphthodianthrones, are important biologically active secondary metabolites of the genus Hypericum. Their biosynthesis is influenced by complex interactions between plants and their endophytic microorganisms, while key steps of their biosynthetic pathway have not yet been completely elucidated. Current models of hypericin biosynthesis are based on interdisciplinary studies, highlighting the need for an integrated approach combining the analysis of metabolomic and transcriptomic data. Despite their structural relatedness, the biosynthetic pathways of anthraquinones in plants and fungi differ substantially in their enzymatic mechanisms as well as in the genomic organization of the corresponding biosynthetic genes. The aim of this dissertation is to evaluate the effect of nanoparticles as alternative abiotic elicitors on the biosynthesis of anthraquinones in plants of the genus Hypericum and in their endophytic fungi. Elicitation-induced changes will be analyzed at the transcriptomic and metabolomic levels. Metabolomic analysis, based on modern analytical approaches including LC-MS/MS, will enable detailed characterization of the chemical profiles of elicited systems and identification of the predominant anthraquinone derivatives. Bioinformatic approaches will be used to support the interpretation of transcriptomic data and to identify candidate biosynthetic genes. The results of this work will contribute to a better understanding of the regulatory mechanisms of anthraquinone biosynthesis in plant in vitro systems and in plant–endophyte systems.
Objective
The aim of the doctoral thesis is to evaluate the effect of nanoparticles as abiotic elicitors on the biosynthesis of anthraquinones in plants of the genus Hypericum and in their endophytic fungi, based on the analysis of changes in the metabolome and transcriptome following elicitation. The identification of key metabolites through the integration of LC-MS/MS analyses and bioinformatic processing of transcriptomic data will contribute to a better understanding of the regulatory mechanisms governing anthraquinone biosynthesis in plant in vitro systems and in plant–endophyte interactions.
References
Current scientific publications in peer-reviewed domestic and international journals indexed in the Web of Science and Scopus databases.
Tutor
doc. RNDr. Katarína Bruňáková, PhD.
Consultant
RNDr. Linda Petijová, PhD.
Title
Targeting the invasive and hypoxia-driven phenotype of PDAC cells with hypericin
Language
SK
Tutor
prof. RNDr. Peter Fedoročko, CSc.
Consultant
RNDr. Viktória Dečmanová, PhD.
Title
Redox modulation and endoplasmic reticulum stress in the sensitization of tumor cells to selected therapeutic approaches
Language
SK
Tutor
prof. RNDr. Peter Fedoročko, CSc.
Consultant
RNDr. Zuzana Jendželovská, PhD.
Title
Exploitation of nanostructures in the modulation of hydrophobic character and therapeutic potential of selected natural secondary metabolites
Language
SK
Tutor
doc. RNDr. Rastislav Jendželovský, PhD.
Molecular Cytology and Genetics (MCGdAj)
Title
Biodiversity and bioprospecting of halophilic archaea from miocene salt deposits
Language
EN
Abstract
Bioprospecting of extreme environments provides clear evidence that extreme conditions naturally select microorganisms with modified biochemistry giving opportunity for new compounds, genes, and processes discoveries. The aim of the project is an in-depth exploration of the uncharted realm of halophilic archaea, focusing on the Miocene salt deposits as a unique and understudied environment. The Miocene salt deposits could serve as a natural repository of ancient genetic material, providing insights into the evolutionary history and ecological roles of halophilic archaea. By combination of advanced molecular techniques and culturing methods, an array of halophilic archaea from these deposits will be isolated and characterized. The bioprospecting potential of these halophilic archaea with applications in modern biotechnology, pharmaceuticals, and sustainable industries will be analyzed. Novel enzymes, biosurfactants, and bioactive compounds will be identified in addressing environmental challenges. The study will contribute significantly to the expanding knowledge of halophilic archaea ecosystems and highlights the protection and sustainable utilization of these microbial resources for future biotechnological advancements.
Objective
The aim of the work is to analyze the population of halophilic archaea from Miocene salt deposits using both cultivation and non-cultivation approaches.
References
McGenity, T.J.; Oren, A. Hypersaline Environments. In Life at Extremes Environments, Organisms and Strategies for Survival; Bell, E.M., Ed.; CAB International: Oxfordshire, UK, 2012
Oren, A. Life in Hypersaline Environments. In Their World: A Diversity of Microbial Environments, Advances in Environmental Microbiology; Hurst, C.J., Ed.; Springer International Publishing: Cham, Switzerland, 2016
Ventosa, A.; Márquez, M.C.; Sánchez-Porro, C.; de la Haba, R.R. Taxonomy of Halophilic Archaea and Bacteria. In Advances in Understanding the Biology of Halophilic Microorganisms; Vreeland, R.H., Ed.; Springer: Dordrecht, The
Netherlands, 2012
Current scientific literature
Tutor
doc. RNDr. Peter Pristaš, CSc., univerzitný profesor
Consultant
RNDr. Lenka Maliničová, PhD.
Title
Ecogenetics and ecogenomics of extreme environments
Language
EN
Abstract
Ecogenetics and ecogenomics are emerging fields that explore the intricate relationships between genetic variation and environmental factors, particularly in extreme environments such as deep-sea vents, polar regions, and salt pans and springs. These extreme conditions exert unique selective pressures that shape the genetic architecture of organisms, driving adaptations at both the phenotypic and molecular levels. The aim of the project is to uncover the mechanisms of adaptation, resilience, and diversity among procaryotic extremophiles by integrating ecological and genomic data. The data obtained will not only enhance our understanding of microorganism’s biodiversity and evolutionary processes but also has should have implications for biotechnological applications, environmental conservation, and understanding potential life forms beyond Earth.
Objective
The aim of the project is to reveal the mechanisms of adaptation, resistance, and diversity among prokaryotic extremophiles by integrating ecological and genomic data. The result of the work will be linage of physicochemical characteristics of the environment with specific genetic and functional adaptations of prokaryotes, thereby contributing to a better understanding of the biodiversity of extreme ecosystems and their potential for biotechnological and environmental applications.
References
Salwan R, Sharma V (2022) Genomics of prokaryotic extremophiles to unfold the mystery of survival in extreme environments. Microbiol Res 264:127156. https://doi.org/10.1016/j.micres.2022.127156
Marzban G, Tesei D (2025) The Extremophiles: Adaptation Mechanisms and Biotechnological Applications. Biology 14(4):412. https://doi.org/10.3390/biology14040412
Rekadwad BN, Li WJ, Gonzalez JM, Punchappady Devasya R, Ananthapadmanabha Bhagwath A, Urana R, Parwez K (2023) Extremophiles: the species that evolve and survive under hostile conditions. 3 Biotech 13(9):316. https://doi.org/10.3390/biology14040412
Tutor
RNDr. Jana Kisková, PhD.
Consultant
doc. RNDr. Peter Pristaš, CSc., univerzitný profesor
Zoology and Animal physiology (ZFZd)
Title
Activation of endogenous mechanisms leading to neuroprotection after stroke
Language
SK
Abstract
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.
Objective
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
References
(1) BONOVÁ, Petra** - KONČEKOVÁ, Jana - NÉMETHOVÁ, Miroslava - MORÁVEK, Marko - BARÁTH, P. - DANCHENKO, M. - BONA, Martin. Remote ischemic conditioning–induced shift from a vulnerable to a tolerant penumbra: A proteomic perspective. In Experimental neurology, 2025, vol. 391 no, p. 115307.
(2) KONČEKOVÁ, Jana - KOTOROVÁ, Klaudia - GOTTLIEB, Miroslav - BONA, Martin - BONOVÁ, Petra**. Changes in excitatory amino acid transporters in response to remote ischaemic preconditioning and glutamate excitotoxicity. In Neurochemistry International, 2024, vol.173, no., p.105658.
(3) Bonova, P., Jachova, J., Nemethova, M., Macakova, L., Bona, M., Gottlieb, M., 2020. Rapid remote conditioning mediates modulation of blood cell paracrine activity and leads to the production of a secretome with neuroprotective features. Journal of neurochemistry 154, 99-111.
(4) Bonova, P., Koncekova, J., Nemethova, M., Petrova, K., Bona, M., Gottlieb, M., 2022. Identification of Proteins Responsible for the Neuroprotective Effect of the Secretome Derived from Blood Cells of Remote Ischaemic Conditioned Rats. Biomolecules 12.
(5) Bonova, P., Nemethova, M., Matiasova, M., Bona, M., Gottlieb, M., 2016. Blood cells serve as a source of factor-inducing rapid ischemic tolerance in brain. The European journal of neuroscience 44, 2958-2965.
(6) Hossmann, K.A., 2012. The two pathophysiologies of focal brain ischemia: implications for translational stroke research. Journal of cerebral blood flow and metabolism : official journal of the International Society of Cerebral Blood Flow and Metabolism 32, 1310-1316.
Tutor
RNDr. Petra Bonová, PhD.
EVI
This topic will be carried out at an external educational institution - Oddelenie neuroregenerácie, plasticity a reparácie, Neurobiologický ústav, Biomedicínske centrum SAV, v. v. i.; https://bmc.sav.sk/veda/vyskumne-skupiny-podla-temy/neurobiologia/ischemia-mozgu/
Title
Biodiversity, osteochronological growth patterns, and changes in genome size of semiaquatic tetrapods during the Turonian Thermal Maximum
Language
SK
Abstract
Temperature-size ecological phenomena, such as temperature-cline rules versus temperature-rise rules, demonstrate that individuals raised at low temperature become larger than conspecifics raised at a higher temperature. Individuals in low-temperature habitats also exhibit increased cell size and genome. The striking variability in genome size between ectotherms and endotherms implies that a temperature effect is involved. Given the verified observation that genome size and cell volume are causally related brings us to the following fundamental questions in the study of fossils: how did the vertebrate cell volume (source for calculating genome size in extinct organisms) relate to environmental temperature during top thermal extremes in the last 100 million years? Could thermal maxima trigger higher extinction rates? Did temperature, as a selective factor, influence the early evolution of modern biota in the Upper Cretaceous and Paleogene? Can we link changes in the size of vertebrate paleogenome with the emergence of new groups of animals or/and innovations within the ancestral lineages? And what is the causal direction between a long-term decrease in body size and a thermal maximum (miniaturization) or post-extinction climate (the Lilliput effect)? The thermal maximum in the Cretaceous (Turonian: 94-93 Myr) and in the Paleogene (Eocene: 55 Myr) and the asteroid impact at the boundary of these periods (K/Pg; Maastrichtian-Paleogene: 65 Myr) significantly influenced the evolution of life on Earth. The sequence of the above global events provides an extraordinary experimental system for assessing the impact of temperature changes on vertebrate evolution. In the doctoral project, we will study this impact at the level of microstructure and developmental rhythm of skeletal tissues of semiaquatic vertebrates, primarily of Turonian age. We will test two hypotheses related to: 1) termoadaptive changes in bone tissue of these ectotherms; and 2) the impact of environmental factors on the genome size of the tetrapods with low versus high disparity. The project will provide original data on the dynamic interaction of life and climate; an evolutionary model of the adaptability of vertebrate morphospace in extreme climatic conditions; and an argumentative basis for assessing conflicting views on current global warming.
Objective
1. Acquisition of fossils and setting up a material base from the Upper Cretaceous localities of Uzbekistan.
2. Establishing database based on synchrotron scans (with micron resolution) of fossil bones of Cretaceous semiaquatic tetrapods and virtual osteohistology analysis.
3. Establishing a virtual model database of synchrotron scans (with submicron resolution) of osteocyte lacunae of Cretaceous continental vertebrates, 3D volumetric reconstruction, and calculation of genome size of individual extinct taxa.
4. Time-calibrated (Upper Cretaceous) correlation of temperature and paleogenomic parameters of semiaquatic tetrapods with low versus high evolutionary disparity.
5. Time-calibrated (Upper Cretaceous) correlation of temperature and histological parameters in the evolutionary morphospace of semiaquatic tetrapods.
6. Formulation of macroevolutionary trends resulting from the results of the project and revision of the current scientific paradigm on the consequences of the last global temperature maxima and the consequences of the impact event on the evolution of life in the northern hemisphere of our planet.
The project will be funded through the project VEGA 1/0259/25 a APVV-24-0161, and other grants provided by the Japan Synchrotron Radiation Research Institute.
References
Angilletta, M. J. et al. 2004. Temperature, growth rate, and body size in ectotherms: fitting pieces of a life-history puzzle. Integr. Comp. Biol. 44(6): 498-509.
Averianov A. P., Sues H. D. 2012. Correlation of Late Cretaceous continental vertebrate assemblages in Middle and Central Asia. J. Stratigr. 36: 462-485.
Billon-Bruyat, J-P. et al. 2016. Oxygen isotope composition of Late Jurassic vertebrate remains from lithographic limestones of western Europe: implications for the ecology of fish, turtles, and crocodilians. Palaeogeograph. Palaeoclimat. Palaeoecol. 3-4: 359-375.
Brinkman, D. B., Tarduno, J. A. 2005. A Late Cretaceous (Turonian Coniacian) high-latitude turtle assemblage from the Canadian Arctic. Can. J. Earth Sci. 42: 2073-2080.
Gregory, T. R. 2005. The Evolution of the Genome. Elsevier Academic Press, Burlington.
Hanken, J., Wake, D. 1993. Miniaturization of body size: organismal consequences and evolutionary significance. Ann. Rev. 24: 501-519.
Johnson, J. et al. 2023. What drives the evolution of body size in ectotherms? A global analysis across the amphibian tree of life. Global Ecol. Biogeogr. 32: 1311-1322.
Skutschas, P. P. 2009. Re-evaluation of Mynbulakia Nesov, 1981 (Lissamphibia: Caudata) and description of a new salamander genus from the Late Cretaceous of Uzbekistan. J. Vertebr. Paleontol. 29: 659-664.
Skutschas, P. P. et al. 2019. Ontogenetic changes in ong-bone histology of the crptobranchid Eoscapherpeton asiaticum (Amphibia: Caudata) from the Late Cretaceous of Uzbekistan. Compt. R. Palevol 18: 306-316.
Secord, R. et al. 2012. Evolution of the earliest horses driven by climate change in the Paleocene-Eocene thermal maximum. Science 335: 959-962.
Thomson, K. S., Muraszko, K. 1978. Estimation of cell size and DNA content in fossil fishes and amphibians. J. Exp. Zool. 205: 315-320.
Wiest, L. A. et al. 2018. Terrestrial evidence for the Lilliput effect across the Cretaceous-Paleogene (K-Pg) boundary. Palaeogeogr. Palaeoclimat. Palaeoecol. 491: 161-169.
Tutor
doc. RNDr. Martin Kundrát, Ph.D.
Consultant
doc. Donald Brinkman, PhD.
Romain Amiot, Ph.D.
Title
Chronological patterns of bone and dental tissue and changes in genome size of the ectotherm and endotherm reptiles during the Turonian Thermal Maximum
Language
SK
Abstract
Temperature-size ecological phenomena, such as temperature-cline rules versus temperature-rise rules, demonstrate that individuals raised at low temperature become larger than conspecifics raised at a higher temperature. Individuals in low-temperature habitats also exhibit increased cell size and genome. The striking variability in genome size between ectotherms and endotherms implies that a temperature effect is involved. Given the verified observation that genome size and cell volume are causally related brings us to the following fundamental questions in the study of fossils: how did the vertebrate cell volume (source for calculating genome size in extinct organisms) relate to environmental temperature during top thermal extremes in the last 100 million years? Could thermal maxima trigger higher extinction rates? Did temperature, as a selective factor, influence the early evolution of modern biota in the Upper Cretaceous and Paleogene? Can we link changes in the size of vertebrate paleogenome with the emergence of new groups of animals or/and innovations within the ancestral lineages? And what is the causal direction between a long-term decrease in body size and a thermal maximum (miniaturization) or post-extinction climate (the Lilliput effect)? The thermal maximum in the Cretaceous (Turonian: 94-93 Myr) and in the Paleogene (Eocene: 55 Myr) and the asteroid impact at the boundary of these periods (K/Pg; Maastrichtian-Paleogene: 65 Myr) significantly influenced the evolution of life on Earth. The sequence of the above global events provides an extraordinary experimental system for assessing the impact of temperature changes on vertebrate evolution. In your doctoral project, we will study this impact at the level of microstructure and developmental rhythm of bone and dental tissue of ectotherm crocodylomorphs and endotherm dinosaurs, primarily of Turonian age. We will test three groups of hypotheses related to: 1) the correlation of circadian dentin increments; 2) adaptive changes in bone tissue; and 3) the impact of environmental factors on the genome size of these vertebrates with low versus high disparity. The project will provide original data on the dynamic interaction of life and climate; an evolutionary model of the adaptability of vertebrate morphospace in extreme climatic conditions; and an argumentative basis for assessing conflicting views on current global warming.
Objective
1. Acquisition of fossils and setting up a material base from the Upper Cretaceous localities of Uzbekistan.
2. Establishing database based on synchrotron scans (with micron resolution) of fossil teeth and bones of Cretaceous crocodylomorphs and dinosaurs and quantitative analysis of the periodicity of dentin increments and cortical zonation.
3. Establishing a virtual model database of synchrotron scans (with submicron resolution) of osteocyte lacunae of Cretaceous crocodylomorphs and dinosaurs, 3D volumetric reconstruction, and calculation of genome size of individual extinct taxa.
4. Time-calibrated (Upper Cretaceous) correlation of temperature and paleogenomic parameters of crocodylomorphs and dinosaurs with low versus high evolutionary disparity.
5. Time-calibrated (Upper Cretaceous) correlation of temperature and histological parameters in the evolutionary morphospace of crocodylomorphs and dinosaurs.
6. Formulation of macroevolutionary trends resulting from the results of the project and revision of the current scientific paradigm on the consequences of the last global temperature maxima and the consequences of the impact event on the evolution of life in the northern hemisphere of our planet.
The project will be funded through the project VEGA 1/0259/25 a APVV-24-0161, and other grants provided by the Japan Synchrotron Radiation Research Institute.
References
Angilletta, M. J. et al. 2004. Temperature, growth rate, and body size in ectotherms: fitting pieces of a life-history puzzle. Integr. Comp. Biol. 44(6): 498-509.
Amiot, R. et al. 2011. Oxygen isotopes of east Asian dinosaurs reveal exceptionally cold Early Cretaceous climates. Proc. Nat. Acad. Sci. 108: 5179-5183.
Averianov A. P., Sues H. D. 2012. Correlation of Late Cretaceous continental vertebrate assemblages in Middle and Central Asia. J. Stratigr. 36: 462-485.
Cavin, L. 2010. Oxygen and carbon isotope compositions of middle Cretaceous vertebrates from North Africa and Brazil: Ecological and environmental significance. Palaeogeogr. Palaeoclimat. Palaeoecol. 297: 439-451.
Finch, S. P., D´Emic, M. D. 2022. Evolution of amniote dentine apposition rates. Biol. Lett. 18: 20220092.
Gregory, T. R. 2005. The Evolution of the Genome. Elsevier Academic Press, Burlington.
Hanken, J., Wake, D. 1993. Miniaturization of body size: organismal consequences and evolutionary significance. Ann. Rev. 24: 501-519.
Martin, J .E. et al. 2014. Sea surface temperature contributes to marine crocodylomorph evolution. Nat. Commun. 5: 4658.
Organ, C. L. et al. 2007. Origin of avian genome size and structure in non-avian dinosaurs. Nature 446: 180-184.
Secord, R. et al. 2012. Evolution of the earliest horses driven by climate change in the Paleocene-Eocene thermal maximum. Science 335: 959-962.
Shedlock, A. M. et al. 2007. Phylogenomics of non-avian reptiles and the structure of the ancestral amniote genome. Proc. Natl Acad. Sci. USA 104: 2767-2772.
Wiest, L. A. et al. 2018. Terrestrial evidence for the Lilliput effect across the Cretaceous-Paleogene (K-Pg) boundary. Palaeogeogr. Palaeoclimat. Palaeoecol. 491: 161-169.
Tutor
doc. RNDr. Martin Kundrát, Ph.D.
Consultant
Romain Amiot, Ph.D.
Title
MICROBIOTA AS A MODULATOR OF THE GUT–KIDNEY AXIS IN KIDNEY TRANSPLANTATION FROM SEPTIC DONORS
Language
SK
Abstract
The shortage of organs suitable for transplantation is forcing transplantation medicine to continuously push the boundaries of donor acceptability criteria. One of the major challenges in contemporary transplant practice is the utilization of kidneys from donors with active sepsis or a history of septic episodes. Although clinical experience suggests that such organs may be viable under certain conditions, the mechanisms influencing their long-term survival and functional integrity remain insufficiently explored. A promising strategy to improve the safety of these transplants is machine perfusion of kidney grafts combined with targeted antibiotic application. This PhD project focuses on elucidating the role of the gut–kidney axis in the context of septic donors. Sepsis induces profound alterations in the intestinal microenvironment, including disruption of the gut barrier and dysregulation of immune responses, which may indirectly yet critically affect the fate of the transplanted organ. The research will be conducted using a large animal model of minipigs, which closely mirrors human physiology and the pathophysiological processes associated with sepsis and kidney transplantation. The PhD candidate will actively participate in the individual experimental phases, enabling a comprehensive evaluation of interactions between gut microbiota, inflammatory responses, and kidney graft function.
Objective
The aim of this PhD thesis is to experimentally evaluate the role of gut microbiota as a modulator of the gut–kidney axis in kidney transplantation from septic donors and to elucidate its impact on inflammatory responses and kidney graft function in the context of machine perfusion with antibiotics.
References
1. Jin, Y., Zhang, S.J., Zhuang, S., Li, P., Miao, H., Zhao, Y.Y. (2026). Microbiota-gut-kidney axis in health and renal disease. International Journal of Biological Sciences, 22(2), 750-770.
https://doi.org/10.7150/ijbs.125140.
2. Evenepoel P, Poesen R, Meijers B. The gut-kidney axis. Pediatr Nephrol. 2017 Nov;32(11):2005-2014. doi: 10.1007/s00467-016-3527-x. Epub 2016 Nov 15. PMID: 27848096.
https://pubmed.ncbi.nlm.nih.gov/27848096/
3. Haak BW, Prescott HC, Wiersinga WJ. Therapeutic Potential of the Gut Microbiota in the Prevention and Treatment of Sepsis. Front Immunol. 2018 Sep 10;9:2042. doi: 10.3389/fimmu.2018.02042. PMID: 30250472; PMCID: PMC6139316. https://pubmed.ncbi.nlm.nih.gov/30250472/
4. Polonio, C.M., Quintana, F.J. Intestinal microbiome metabolites control sepsis outcome. Nat Immunol 26, 155–156 (2025). https://doi.org/10.1038/s41590-024-02050-1
5. Moers, C., Smits, J.M., Maathuis, M.H.J., Treckmann, J., van Gelder, F., Napieralski, B.P., van Kasterop-Kutz, M., van der Heide, J.J.H., Squifflet, J.P., van Heurn, E., et al. (2009) Machine perfusion or cold storage in deceased-donor kidney transplantation. New England Journal of Medicine, 360(1), pp. 7–19. https://doi.org/10.1056/NEJMoa0802289
6. Simsek C, Karatas M, Tatar E, Yildirim AM, Tasli Alkan F, Uslu A. Kidney Transplantation From Infected Donors With Particular Emphasis on Multidrug-Resistant Organisms: A Single-Center Cohort Study. Exp Clin Transplant. 2022 Mar;20(Suppl 1):61-68. doi: 10.6002/ect.MESOT2021.O25. PMID: 35384809
https://www.ectrx.org/detail/supplement/2022/20/3/1/61/0
Tutor
RNDr. Vlasta Demečková, PhD., univerzitná docentka
Title
Molecular mechanisms of early embryo cell responses to the factors of environment
Language
SK
Abstract
The mammalian preimplantation embryo (i.e. the embryo in the period from oocyte fertilization to implantation of blastocyst into uterus) can finish its development to the blastocyst stage relatively autonomously and in in vitro conditions in relatively simple culture media. On the other hand, recent data indicate that disturbed maternal environment significantly affects developmental potential of oocytes, quality of pre-implantation embryos, success of implantation and can be the cause of unsuccessful pregnancies in both humans and animals. Moreover, in line with the DOHaD (Developmental Origin Health and Diseases) hypothesis, impairment of early embryonic development can also have long term consequences for health in adulthood. The research will mainly focus on the role of low molecular weight ligands and their receptors. The experiments will mostly use a mouse model (in vivo as well as in vitro approaches, including mouse embryonic stem cells). Modern biochemical methods, molecular biology techniques as well as morphological methods will be used to analyze cell receptors, activated signaling pathways and physiological responses of early embryo cells.
Objective
1) To analyze the expression of selected cell receptors binding low molecular weight ligands in preimplantation embryos
2) To analyze the impact of activation of identified cell receptors on early embryonic cells
3) To analyze the possible long-term effects of activation of identified cell receptors on the physiological / health status of the offspring
References
DePamphilis M. 2016. Mammalian preimplantation development. Academic Press, Elsevier, 447pp.
Leese HJ and Brison DR. 2015 Cell Signaling during mammalian early embryo development. Springer, 213pp.
Niakan KK et al. Human pre-implantation embryo development. Development. 2012 Mar;139(5):829-41. doi: 10.1242/dev.060426.
Leese HJ .Metabolism of the preimplantation embryo: 40 years on. Reproduction 2012 Apr;143(4):417-27. doi: 10.1530/REP-11-0484.
Duranthon V et al. Preimplantation embryo programming: transcription, epigenetics, and culture environment. Reproduction 2008 Feb;135(2):141-50. doi: 10.1530/REP-07-0324.
Tutor
RNDr. Štefan Čikoš, DrSc.
Consultant
RNDr. Alexandra Špirková, PhD.
EVI
This topic will be carried out at an external educational institution - Ústav fyziológie hospodárskych zvierat, Centrum biovied SAV, v.v.i., Košice, Šoltésovej 4-6
Title
AUTISM SPECTRUM DISORDERS AND GUT–BRAIN AXIS DYSREGULATION: EXPERIMENTAL MODULATION VIA FECAL MICROBIOTA TRANSPLANTATION AND NATURAL ADDITIVES
Language
SK
Abstract
Autism spectrum disorders (ASD) are complex neurodevelopmental conditions increasingly associated with disturbances in gut microbiota and dysregulation of gut–brain axis communication. Numerous studies suggest that intestinal dysbiosis may contribute not only to frequent gastrointestinal issues in individuals with ASD but also to behavioral disorders and immune imbalance. This dissertation project focuses on the experimental modulation of gut dysbiosis using fecal microbiota transplantation (FMT) from children with ASD, as well as natural additives – specifically probiotics and prebiotics. Using a mouse model, we investigate the effects of these interventions on systemic and intestinal immune responses, inflammatory processes, hematological parameters, and gene expression in colonic tissue. If you are interested in research that bridges immunology, neuroscience, and microbiology, this is a unique opportunity. To explore the mechanisms underlying these disorders, we will employ state-of-the-art molecular biology techniques such as high-throughput next-generation sequencing (NGS), RNA-seq, and other advanced analytical approaches. Join us in research that may open up new therapeutic strategies and significantly shape the future of medicine.
Objective
The main objective is to experimentally evaluate the impact of fecal microbiota transplantation (FMT) from children with autism spectrum disorders (ASD), followed by therapeutic intervention using natural additives (probiotics and prebiotics), on gut dysbiosis, immune and inflammatory responses, hematological parameters, and gene expression in a mouse model of ASD.
Tutor
RNDr. Vlasta Demečková, PhD., univerzitná docentka
Title
Regulation of neurogenesis in the adult brain
Language
SK
Abstract
The largest neurogenic region in the adult brain is the subventricular zone (SVZ) of the lateral ventricles. Neurons originating in the SVZ migrate long distances along the rostral migration pathway (RMS) to the olfactory bulb (OB), where they integrate into existing neuronal circuits. Understanding the mechanisms regulating adult neurogenesis is essential for its potential therapeutic use. The aim of the dissertation will be to investigate the mechanisms regulating cell proliferation, migration and differentiation in the SVZ-RMS-OB system based on histological and in vitro methods and behavioral testing.
Objective
Investigation of the mechanisms regulating cell proliferation, migration and differentiation in the neurogenic region SVZ-RMS-BO of the adult rat brain, based on histological and in vitro methods and behavioral testing.
References
(1) Saghatelyan A. Role of blood vessels in the neuronal migrtion. Semin. Cell Dev. Biol. 2009, 20:744-750.
(2) Lim, D.A., Alvarez-Buylla A. The adult ventricular-subventricular zone (V-SVZ) and olfactory bulb (OB neurogenesis. Cold Spring Harb. Perspect Biol. 2016, 8a018820.
(3) Garcia-González, D., Khodosevich, K., Watanabe, Y., Rollenhagen, A., Lübke, J.H.R., Monyer H. Serotonergic projections govern postnatal neuroblast migration. Neuron 2017,94:534-549.
(4) Martončíková, M., Alexovič Matiašová, A., Ševc, J. Račeková, E. Relationship between blood vessels and migration of neuroblasts in the olfactory neurogenic region of the rodent brain. Int. J. Mol. Sci. 2021, 11506.
(5) Angelidis, A., Račeková, E., Arnoul, P., Závodská, M., Raček A., Martončíková, M. Disrupted migration and proliferation of neuroblasts after postnatal administration of angiogenesis inhibitor. Brain Res. 2018, 1698:121-129.
Tutor
RNDr. Marcela Martončíková, PhD.
EVI
This topic will be carried out at an external educational institution - NbÚ BMC SAV - Oddelenie regeneračnej medicíny a bunkovej terapie, Neurobiologický ústav, Biomedicínske centrum SAV, v. v. i.; https://bmc.sav.sk/veda/vyskumne-skupiny-podla-temy/neurobiologia/regeneracna-medicina-a-bunkova-terapia/
Title
The succession of soil Collembola communities in spruce forests of the High Tatra Mountains (Slovakia) - twenty years after a windthrow
Language
SK
Abstract
Windthrow, as one of the natural disturbance factors, plays an important role in the successional cycle of natural montane forests, affecting their structure, resources and microclimate. These changes in forest ecosystems significantly influence soil arthropod communities. Knowledge on the response of soil biota to such natural disturbances and soil fauna regeneration in montane ecosystems are scarce. The windstorm devastated the forest ecosytem in mountain area of the Tatras (National Park of High Tatras, Sloavakia) 20 years ago. In this context, the impact of windthrow and the forestry (management) practices on the structure and community abundance of soil Collembola will be investigated over time. Collembola can serve as sensitive indicator mesofauna group in assessments of disturbance-induced changes in soil environments of mountain forests. Goal of the PhD. thesis is to assess „the recovery“ of soil Collembola communities in mountain spruce forests in the High Tatra Mts., 20 years after a windthrow, and to compare these communities in relation to different forestry practices.
Objective
1) To assess the recovery of soil Collembola communities in mountain spruce forests in the High Tatra Mts., 20 years after a windthrow.
2) To compare these communities in relation to different practices within of forest management.
References
Coleman, D.C., Callaham, M.A., Crossley, D.A., 2017. Fundamentals of soil ecology: third edition. Fundam. Soil Ecol. Third Ed.
Hopkin, S.P., 1997. Biology of the springtails (Insecta: Collembola), Oxford
Huhta, V., 1976. Effects of clear-cutting on numbers, biomass and community respiration of soil invertebrates. Ann. Zool. Fenn. 13.
Flórián N., Gergócs-Winkler V., Kovács B., Aszalós R., Bidló A., Ódo P., 2025. Effects of different forestry management practices on soil mesofauna in the regeneration phase. Forest Ecology and Management, 598: 123196. https://doi.org/10.1016/j.foreco.2025.123196
Thom, D., Seidl, R., 2016. Natural disturbance impacts on ecosystem services and biodiversity in temperate and boreal forests. Biol. Rev. Camb. Philos. Soc. 91.
Wallwork, J.A. 1970. Ecology of Soil Animals. McGraw-Hill, England, 283 pp.
Tutor
RNDr. Natália Raschmanová, PhD., univerzitná docentka
Consultant
prof. RNDr. Ľubomír Kováč, CSc.
Title
Genome size of some gropus of soil, cave and aquatic arthropods in evolutionary and ecological context
Language
SK
Abstract
Measuring intra- and interspecies genome size (nuclear DNA) using flow cytometry (FCM) is a widely used rapid tool to distinguish taxonomic, reproductive, and adaptive differences between organisms, so far mainly utilized in plant biology. However, a number of studies also point to the potential use of FCM in the study of animals. Genome size evolution has its own regularities and does not follow a linear trend. Genome enlargement is often associated with polyploidization and the hybrid origin of species. These two fundamental evolutionary processes lead to the emergence of genomes with a broader range of genetic material, enabling faster adaptive responses of living organisms to environmental changes. The genome size database (https://www.genomesize.com/) provides an excellent overview of current knowledge and literature sources. At the same time, it shows further possibilities. Some groups of animals in this area are almost unexplored. This work will focus mainly on crustaceans and millipedes, obtained from soil, caves, and aquatic environments. For crustaceans and millipedes, we have recently standardized a protocol (method of fixation, nucleus isolation, and nuclear DNA staining), which is not universally applicable. The study will test intraspecific genome variability (between sexes, within a population, and between populations), examine potential polyploidy and endopolyploidy, and explore correlations between the phylogenetic positions of species, differences between closely related and distant species, body size, preferred environment and adaptability of species, biogeography, and genome size. Material will be collected in the field during ecological research of the training center and field excursions, as well as from breeding (exotic species).
Objective
1) Creating of datasets of nuclear DNA size measurements by flow cytometry and examine the range of genome size variability in selected taxa of arthropods, particularly myriapods (Myriapoda) and crustaceans (Crustacea), and investigate trends in genome size evolution in these groups.
2) Investigate the variability in genome size of selected taxa in relation to the morphology of their bodies and individual organs, their ecological requirements, and life strategies.
3) Apply flow cytometry as a tool enabling a deeper understanding of the background of biodiversity associated with climatic microrefugia.
References
Alfsnes, K., Leinaas, H.P., Hessen, D.O. (2017) Genome size in arthropods; different roles of phylogeny, habitat and life history in insects and crustaceans. Ecology and Evolution, 7: 5939–5947.
Brown, T.A. (2002) Genomes, 2nd edition. BIOS Scientific Publishers, Oxford, 572 s.
Freeland, J.R. (2020) Molecular Ecology. 3rd Editon. Willey Blackwell, 384 s.
Gregory, T.R. (2005) The Evolution of the Genome. Elsevier Academic Press, Inc., London, 768 s.
Gregory, T.R. (2026) Animal Genome Size Database. http://www.genomesize.com.
Gregory, T.R., P. Nathwani, T.R. Bonnett, and D.P.W. Huber (2013) Sizing up arthropod genomes: an evaluation of the impact of environmental variation on genome size estimates by flow cytometry and the use of qPCR as a method of estimation. Genome 56: 505–510.
Jeffery, N. W., and T. R. Gregory (2014). Genome size estimates for crustaceans using Feulgen image analysis densitometry of ethanol-preserved tissues. Cytometry Part A 85: 862-868
Ruppert, E.E., Fox, R.S., Barnes, R.D. (2004) Invertebrate Zoology. 7th Edition. Brooks/Cole Cengage Learning, 1008 s.
Shapiro, J.A. (2023) Engines of innovation: biological origins of genome evolution, Biological Journal of the Linnean Society, Volume 139 (4): 441–456.
Thomas, G.W.C., Dohmen, E., Hughes, D.S.T. et al. (2020) Gene content evolution in the arthropods. Genome Biol 21, 15.
Tutor
doc. RNDr. Andrej Mock, PhD.
Consultant
doc. Mgr. Vladislav Kolarčik, PhD.
Title
The influence of microclimate on oribatid mite communities (Acari, Oribatida) along gradients in the entrance zone of cold caves on a broader geographical scale
Language
SK
Abstract
Natural microclimatic gradients in cold cave entrances with temperature and vegetation inversions reveal high a-diversity of oribatid mites (Acari, Oribatida). Cave entrances represent relatively stable and heterogeneous habitats characterized by environmental gradients determined by their topology and morphology. Such habitats may serve as crucial microrefugia for endemic and relict arthropods. The ecotonal environment of cave entrances, where subterranean and surface habitats overlap, has remained understudied regarding its significance for the local biodiversity of small soil arthropods. The diversity, structure, and ecology of oribatid mite assemblages, and their relationship to microclimatic and edaphic conditions, will be investigated along transects from cave entrances to adjacent forest habitats within a broader geographical context, encompassing selected localities in the Carpathians, Alps, Dinaric mountains and Caucasus Mts.
Objective
1) To assess the diversity and community composition of oribatid mites within the microclimatic gradients of cave entrances, focusing on selected sites in the Carpathian, Dinaric, Alpine, and Caucasian regions.
2) To assess the distribution of oribatid functional groups in relation to the microclimatic and topographical heterogeneity of cave entrance habitats.
References
Behan-Pelletier V., Lindo, Z. 2023. Oribatid mites. Biodiversity, Taxonomy and Ecology. CRC Press, Boca Raton, 494 pp.
Gaston, K. J. 2000. Global patterns in biodiversity. Nature, 405(6783), 220–227.
Margesin, R., Schinner, F. 1999. Cold-Adapted Organisms—Ecology, Physiology, Enzymology and Molecular Biology. Springer-Verlag, Berlin, 416 pp.
Petrovová, V., Ľuptáčik, P., Kolarčik, V., Kováč, Ľ., 2024: Biodiversity of a temperate karst landscape - ice cave collapse doline supports high α-diversity of the soil mesofauna. Scientific Reports, 14: 22205.
Salazar-Fillipo et al. 2025. Changes in trait assemblages of oribatid mite communities during natural succession on post-mining sites. European Journal of Soil Biology 127, 103777.
Wallwork, J.A. 1970. Ecology of Soil Animals. McGraw-Hill, England, 283 pp.
Walter, D.E., Proctor, H.C. 2013. Mites: Ecology, Evolution & Behaviour. Springer, Dordrecht, 494 pp.
Tutor
prof. RNDr. Ľubomír Kováč, CSc.
Consultant
RNDr. Peter Ľuptáčik, PhD.
Title
Origin and adaptive patterns of secondary flightlessness: an alternative evolution of birds
Language
SK
Abstract
The transformation of the forelimb into a dominant locomotor organ characterizes the evolution of Paraves species, including modern birds. This adaptive transformation occurred independently, in several clades, and in different ways. Although the flapping wing became the dominant support for active flight, the secondary loss of this ability occurred frequently in bird evolution. The evolution of flightlessness is associated with several ecological, physiological, and morphological phenomena, which reflect adaptive requirements of a ground-dwelling lifestyles. The goal of our research is to understand how the loss of flight affects body proportions, especially wing polymorphism, at the microstructure level of bone tissues. For example, how do developmental heterochronies contribute to the diversity and functionality of wings and legs in partially or completely flightless birds? Within the framework of accelerated somatic maturation, we will investigate the hypothesis of multi-rate skeletal organ development that enabled the adaptive transition to flightlessness, and why the loss of flight led to gigantism in some birds, while not in others. We aim to map these adaptive specializations within the evolutionary phylomorphospace and to examine the temporal and topological constraints on the evolution of flightless birds.
Objective
1. Phylogeographic mapping of the occurrence of loss of active flight in the evolution of Avialae;
2. Developmental anatomy and osteohistology to understand the flightless Palaneognathae model vs the flightless Neognathae model;
3. Study adult wing and leg bone morphology and histology in flightless birds in relation to gigantism;
4. Defining microstructural and functional adaptation trends of the wing in the evolution of secondary flightless birds.
The project will be funded through the project VEGA 1/0259/25 a APVV-24-0161, and other grants provided by the Japan Synchrotron Radiation Research Institute (16A-1038/32694 a 18B-1543/42978).
References
Heck, C. T., Woodward, H. N. 2021. Intraskeletal bone growth patterns in the North Island Brown Kiwi (Apteryx mantelli): Growth mark discrepancy and implications for extinct taxa. J. Anat. 239: 1075-1095.
Kundrát , M. 2009. Primary chondrification foci in the wing basipodium of Struthio camelus with comments on interpretation of autopodia elements in Crocodilia and Aves. J. Exp. Zool. 312B: 30-41.
de Ricqlès, A. et al. 2016. Preliminary assessment of bone histology in the extinct elephant bird Aepyornis (Aves, Palaeognathae) from Madagascar. C. R. Palevol. 15: 197-208.
Sackton, T. B. et al. 2019. Convergent regulatory evolution and loss of flight in paleognathous birds. Science 364: 74-78.
Turvey, S. T. et al. 2005. Cortical growth marks reveal extended juvenile development in New Zealand moa. Nature 435: 940-943.
Worthy, T. H. et al. 2017. The evolution of giant flightless birds and novel phylogenetic relationships for extinct fowl (Aves, Galloanseres) R. Soc. Open Sci. 4: 170975.
Wright, N. A. et al. 2016. Predictable evolution toward flightlessness in volant island birds. Proc. Natl. Acad. Sci. USA 113: 4765-4770.
Young, J. J. et al. 2019. Attenuated Fgf signaling underlies the forelimb heterochrony in the emu Dromaius novaehollandiae. Curr. Biol. 29: 3681-3691.e5
Tutor
doc. RNDr. Martin Kundrát, Ph.D.
Consultant
prof. Luís Fábio Silveira, Ph.D.
Dr. Thomas L. Stubbs, Ph.D.