Original title in Czech: Biofyzikální chemieFaculty: FCHAbbreviation: DPCP_BCHAcad. year: 2021/2022
Type of study programme: Doctoral
Study programme code: P0531D130045
Degree awarded: Ph.D.
Language of instruction: Czech
Accreditation: 8.10.2019 - 8.10.2029
Mode of study
Standard study length
prof. Ing. Miloslav Pekař, CSc.
doc. Ing. Adriána Kovalčík, Ph.D., doc. Ing. Filip Mravec, Ph.D., doc. Ing. Stanislav Obruča, Ph.D., prof. RNDr. Ivana Márová, CSc., prof. Ing. Martina Klučáková, Ph.D.
prof. RNDr. Jiří Doškař, CSc., prof. Mgr. Marek Koutný, Ph.D., doc. RNDr. Jaroslav Turánek, CSc., prof. RNDr. Zbyněk Zdráhal, Dr.
Fields of education
Issued topics of Doctoral Study Program
- A physico-chemical contribution to discussion on soil organic matter
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. After additional but in-depth literature search, the PhD study will be focused on one of or both following partial goals. 1) Thermodynamics and kinetics of the soil metabolic reactions with special regard to the synthesis of polyketides and their potential incorporation into the principal structural unit of the soil organic matter. 2) Colloid structures in the soil solution or in the soil aqueous leachates, their size, stability, diffusion behavior, aggregate character, chemical composition. Just hydrocolloids and water-soluble molecules are accessible to plants and thus are among key factors enabling and controlling their development and growth. Results will be evaluated also from the point of view of the current discussion on the origin, character, and stability of soil organic matter.
- Analysis of DNA binding proteins with a focus on their interaction with local DNA structures
Local DNA structures play an important role in basic cellular processes such as replication and transcription. Recently, the presence of G-quadruplexes in DNA has been shown to be important for regulation in the cell, but also in the regulation of the life cycle of various viruses (HIV, HSV, EBV). These local structures are recognized by a variety of proteins. In this dissertation thesis, protein interactions with local DNA structures will be studied with a focus to cruciforms and quadruplex DNA. Physical, biochemical and molecular biological methods including the isogenic yeast system will be used to study the recognition of target structural motifs in the gene promoter region. Microscopic methods including confocal microscopy will also be used to study localization and interactions in cellular systems.
- Application of complex microbial and plant extracts in food and cosmetics
This thesis is focused on preparation and characterization of natural microbial, algal and plant extracts containing vitamins, provitamins, antioxidants and glucans. The main goal is to evaluate a complex biological effect of these extracts and their mixtures and application potential to some food and cosmetic products. Extracts will be stabilized by encapsulation into different types of organic micro- and nanoparticles and fibres. Characterization of application forms will be performed by microscopy, chromatography and spectroscopy. As a part of thesis development of methods for analysis of active substances as well as testing biological effects and safety (EFSA rules) will be solved. Long-term stability in model and real foods and model physiological conditions will be evaluated. Cytotoxicity and biocompatibility will be studied using cell cultures.
- Bioinformatics and biophysical characterization of local structures from genomic sequences of nucleic acids
not offered in English programme
- Biophysical characterization of polyhydroxyalkanoates in-vivo and ex-vivo
The focus of this thesis is the analysis of physicochemical properties of bacterial polyesters polyhydroxyalkanoates (PHA) with respect to their native form in bacterial cells (in-vivo) as well as concerning the characterization of the materials after extraction from the bacterial cell (ex-vivo). The goal is to understand the unique properties of these materials in the context of their biological functions and design and test employment of the materials in advanced applications (delivery systems, medical applications etc.).
- Fluorescence spectroscopy in the study of properties of associative colloidal systems
This work is focused on the use of stationary, time resolved and microscopic fluorescence techniques in research of physical properties of associative colloids. The information obtained will be correlated with technological parameters of associative colloids such as solubilization and solubilization capacity, stability, size distribution, etc. The study will acquire not only skills in various techniques of fluorescence spectroscopy, but also in comparative techniques such as light scattering techniques.
- Hydrogels for medical applications – rheology, diffusion and rational design strategies
Hydrogels constitute a versatile platform for a variety of biomedical applications – for example, in the drug delivery, as extracellular matrix models, or in tissue engineering. When developing new hydrogels, design rules are still lacking and the development relies largely on trial and error approach. This thesis will make a step in progress in this direction – it will focus on the rheological and transport properties of hydrogels followed by formulating some rules for the strategy of their rational design. At the start, a sufficiently thorough literature search will be made and focused on the published preparation methods for biomedical hydrogels and on the data on their rheological and transport properties. Based on the meta-analysis of the published data a first draft, at least, of the desired rules will be formulated and experiments designed and then performed which will complete and verify the rules. The experiments will make a comparison of different hydrogel matrices for the same drug or model molecule, especially their rheological and transport properties including the release profiles and their mathematical modeling. Depending on the possibility of external cooperation, in vivo release studies will be also realized. The obtained findings will be summarized in the rules for hydrogel design strategies.
- Mobility and reactivity of pharmaceuticals in soil ecosystems
Study of interactions of hormones and drugs with soil organic matter, stability of formed complexes. Study of transport of hormones and drugs in model and real soils. Study of relationships between reactivity, mobility and bio-availability of pharmaceuticals.
- Modelling of transport phenomena in biological environment
The development of various drug delivery systems is an area of active research. This research is focused mainly on chemical, biochemical, or physiological aspects. The movement of a delivery system in human body, to the point of the drug action is much less investigated. The drug transport to the targeted site where the drug’s chemical action should take place is essential for its proper function. This study will be therefore aimed at mathematical modeling of this transport based either on published data or data collected at the supervisor’s laboratory. The work will be focused on the modeling of the diffusion of nano- and microparticles in model biological medium, especially in hydrogel or similar model of the extracellular matrix, or through biological membrane. These tasks will be solved using COMSOL packet. The tasks include also the construction of realistic structural model of the environment and the modelling support of the microrheological experiments in hydrogels performed in the laboratory where this PhD study will be realized. The aim of this study is obtaining a feedback for the design of the drug delivery systems.
- Preparation and characterization of conductive hydrogels based on polyhydroxyalkanoates
The focus of the work is the preparation of conductive hydrogels based on polyhydroxyalkanoates (PHAs). Conductive hydrogels have great potential, especially in electronics, biomedicine and tissue engineering. PHAs are biodegradable and biocompatible biopolymers. The aim of the work is to develop a method for the synthesis of low molecular weight PHA, which would be accessible for the modification of functional groups. Two methodologies for preparing low molecular weight PHA will be followed: 1) direct biosynthesis of low molecular weight mcl-PHAs and 2) molecular weight reduction by chemical synthesis. Hydrogels will be synthesized from the modified PHA. Hydrogels will be characterized in terms of their ability to absorb and desorb water as well as the gradual release of drugs. In addition to thermal, rheological, mechanical and electrical properties, their toxicity and the extent of possible biodegradation will be investigated.
- Study of the plasma activated water application on soil organic components
The environmentally friendly farming methods and procedures became a hot topic during the last years. One of possible ways is the application of plasma activated water. Water exposed to plasmas contains not only oxidative species (mainly hydrogen peroxide) but also species with antibacterial and fungicide properties (like peroxynitrile), all in dependence on plasma conditions. Moreover, it is possible to generate nitrites and nitrides that can be applied in form of spray through on leaves as fertilizers. A part of this spray terminates on soil and there is unknown up to now how this application changes the soil properties, especially properties of soil organic parts. The PhD study will be dialled on the detail study of plasma activated water application on different soil types with focus on the soil organic matter and microorganisms. The experimental work will use diagnostics available not at home faculty, only, but also at other European laboratories under the frame network of COST Action CA19110. The work will be continuously discussed with soil specialists from Mendel University in Brno.
Course structure diagram with ECTS credits
|DC_BCHBM||Biophysics and Biochemistry of Microorganisms||cs||0||Compulsory-optional||Col||yes|
|DC_F3D||Photochemistry and 3D print||cs||0||Compulsory-optional||Col||yes|
|DC_MT||Material technology for the biophysical and medical applications||cs||0||Compulsory-optional||Col||yes|
|DC_KPD||Advanced Colloid Chemistry||cs||0||Compulsory-optional||Col||yes|
|DC_PFT||Advanced fluorescence techniques||cs||0||Compulsory-optional||Col||yes|
|DC_PTT||Advanced techniques of thermal analysis||cs||0||Compulsory-optional||Col||yes|
|DC_SMB||Special molecular biotechnology||cs||0||Compulsory-optional||Col||yes|
|DC_STI||Special techniques of instrumental analysis||cs||0||Compulsory-optional||Col||yes|
|All the groups of optional courses|