Full-time study

4 years

prof. Ing. Miloslav Pekař, CSc.

Chairman :
prof. Ing. Miloslav Pekař, CSc.
Councillor internal :
prof. Ing. Martina Klučáková, Ph.D.
doc. Ing. Filip Mravec, Ph.D.
prof. Ing. Stanislav Obruča, Ph.D.
prof. Ing. Adriána Kovalčík, Ph.D.
prof. RNDr. Ivana Márová, CSc.
Councillor external :
prof. Mgr. Marek Koutný, Ph.D.
prof. RNDr. Zbyněk Zdráhal, Dr.
Ing. Lukáš Nejdl, Ph.D.
prof. RNDr. Dalibor Štys, CSc.
prof. RNDr. Jaroslav Turánek, CSc.

1. Biocolloidal hydrogels for study of mobility of reactive particles

   Suitable biocolloids as active substances for the preparation of hydrogels will be chosen on the basis of literature review. Rheological and transport properties will be studied.

   Tutor: Klučáková Martina, prof. Ing., Ph.D.

2. Dissolved organic matter in soils – biocolloidal approach

   Soil organic matter, in a narrower sense, humic substances, has been subject of research for several centuries. Nevertheless, questions on its formation or character still have not been resolved. The traditional polymer theory seems to be replaced in the last two decades by supramolecular views, lately claims on the non-existence of the humic substances have become rampant, looking at the soil organic matter as a complex mixture of products at various degrees of the decomposition of decaying original plant or animal matter. Further, it can contain also metabolic products of the soil microorganisms. Dissolved organic matter is crucial for (nutrients) uptake by plants and their development and growth. This matter is rather overlooked in the ongoing discussion that is focused more on solid soil matrix or its traditional isolates – the humic and fulvic acids. After additional but in-depth literature search, the PhD study will be focused on the formation and occurrence of colloidal structures in the soil solution or in the soil aqueous leachates. The study will focus on the aggregation behavior and character of dissolved organic matter, on the size, stability, and diffusion behavior of colloidal structures, possibility to distinguish the supramolecular or macromolecular characters. The study can include also a model study of the colloidal behavior of well-defined molecules which were revealed in soil solutions. Results will be evaluated just from the point of view of the current discussion on the origin, character, and stability of soil organic matter.

   Tutor: Pekař Miloslav, prof. Ing., CSc.

3. FCS study of structural and transport properties of hydrogels

   Hydrogels represent a broad class of materials with diverse applications in biomedicine, environmental science, agrochemistry, and other fields. In these applications, research predominantly focuses on the reservoir properties of these materials, specifically the correlation between their internal porous structure and transport characteristics. Due to their high water content and low solid content, studying these systems in their native, hydrated state presents significant challenges. Fluorescence correlation spectroscopy (FCS) offers a particularly suitable approach for investigating structural and transport properties, providing insights into the local diffusion behavior of fluorescent molecules or complexes. This study aims to establish a correlation between the diffusion behavior of selected model systems/particles within the hydrogel network and their surrounding environment. This will involve investigating the transport of these systems into and out of the hydrogel, as well as their movement within the hydrogel matrix itself. The study will employ a range of complementary techniques, including light scattering and various microscopy methods such as time-resolved fluorescence microscopy (TRFM), electron microscopy (EM), and atomic force microscopy (AFM). This research will provide in-depth knowledge of fluorescence spectroscopy and microscopy techniques, as well as methods for characterizing hydrogel matrices.

   Tutor: Mravec Filip, doc. Ing., Ph.D.

4. Hydration of biocolloids

   Study of hydration of several biocolloids (e.g. chitosan, hyaluronic acid, humic substances) by means of several methods chosen on the basis of students' review, study of phenomenons related to interactions of biocolloids with water and aqueous solutions (dissolving, dissociation).

   Tutor: Klučáková Martina, prof. Ing., Ph.D.

5. Optical microscopy for imaging and counting nanoscale entities of biological origin

   Either absolute or relative methods can be used for estimating the molar concentrations of molecules and the number concentrations of nanoparticles. Absolute methods are attractive because they do not require calibration. During the calibration, the analytical signals such as absorbance, fluorescence, electric current, etc., are related to calibration standards. Indeed, this is error-prone scrutiny with an inevitable need for repeating. Additionally, calibration cannot always be made because calibration standards are unavailable for many analytes or substances. The recent development of methods for counting single nanoscale entities such as molecules and nanoparticles has exceptional opportunities for absolute and sensitive analysis. The dissertation focuses on adapting optical microscopy to count nanoscale entities from liquid dispersions and estimate their molar and number concentrations. Different imaging modalities such as bright-field, fluorescence, and photon-upconversion microscopies are tested. New techniques are developed for linking the counted numbers with sampled volumes – a critical step for estimating the molar and number concentrations. The methods are tested on purified model molecules and nanoparticles of known concentration and compared to reference methods. The analytical characteristics such as the limit of detection and working range are evaluated. The applicability for analysis of biological nanoscale entities is considered and evaluated experimentally. The absolute quantification of biological polymers, cell inclusions, and fluorescent molecules is tested. Finally, the capabilities of developed methods are discussed in the context of the recent literature.

   Tutor: Hlaváček Antonín, Mgr., PhD

6. Polysaccharides as suitable transport and signaling biomolecules for the preparation of drug carrier systems

   Nowadays, we can see great progress in the synthesis of new drugs for very serious diseases narrowing the human society, such as oncological, autoimmune or genetic diseases. However, new drugs are very often limited by their not very good physicochemical properties, such as solubility in aqueous media, etc... These physicochemical limits can be overcome in the search for new carrier systems capable of addressing these obstacles. The topic of this dissertation is devoted to the search for new carrier systems based on biocompatible polysaccharides as transport media for highly hydrophobic drugs or their model compounds. The scope of the thesis will be to prepare specific drug carrier systems using covalent and weak bonding interactions between the biopolymer and the drug or its model compound. Furthermore, the behavior of these systems in aqueous environments will be studied, including in approximations such as the internal environment of the human body. The transport and stability behavior of these systems will also be added to this dissertation. The aim is to obtain feedback for the creation and design of specific carrier systems.

   Tutor: Enev Vojtěch, doc. Ing., Ph.D.

7. Study on the dynamics and ecological impacts of fragmentation of persistent and biodegradable polyesters in different ecosystems.

   The shift from conventional synthetic polymers to biodegradable alternatives in plastics production brings with it not only the promise of a lower long-term environmental burden, but also some complex environmental issues. The focus of this thesis works with the hypothesis that the actual ecological impact of replacing conventional polymers with biodegradable alternatives represents a complex trade-off between short-term and long-term environmental effects. The release of secondary nanoplastics during polymer degradation is an example of a short-term negative effect that requires consideration in a broader temporal context. The experimental scope of the study will include a comparative analysis of the release of micro- and nanoparticles from conventional and biodegradable polyesters and their effect on the physical, chemical and biological properties of model environments, namely soil, compost and selected aquatic ecosystems. The research includes the artifactual preparation and characterization of the particles, model experiments aimed at simulating abiotic and biotic conditions for their release in natural systems, and the evaluation of the short-term toxicity of these particles. The topic of this thesis complements the experimental study of biodegradation and natural degradation of these polymeric materials already underway in a long-term time perspective. Thus, the aim of the PhD thesis will be not only to understand the mechanisms of fragmentation, but also to quantify the ecological burden of materials based on persistent or biodegradable polyesters. The main motivation of the thesis is to contribute to the reasonable and sustainable use of biodegradable materials by assessing the realistic trade-off between positive and negative effects in the short and long term.

   Tutor: Sedláček Petr, doc. Ing., Ph.D.

8. The role of local nucleic acid structures in the regulation of senescence and aging

   Senescence is a complex biological process influenced by many factors, including genetic and epigenetic ones. Local nucleic acid structures, such as G-quadruplexes, may contribute significantly to the regulation of gene expression and thus influence the aging process. In this work, we focus on the study of the relationship between the structure and function of these structures in the context of senescence and aging. Using bioinformatics tools, we identify potential sites for G-quadruplex formation in the genomes of model organisms. Subsequently, these structures will be characterized using biophysical methods. Furthermore, the interactions of these structures with proteins and their influence on the regulation of gene expression will be studied. At the cellular level, the functional consequences of stabilization or destabilization of these structures by interacting molecules will be investigated. We foresee collaboration with a foreign institute specialising in the study of senescence.

   Tutor: Brázda Václav, prof. Mgr., Ph.D.