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. 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.

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

2. Analysis of non-canonical nucleic acid structures and their medical significance

   Local structures in DNA play an important role in basic cellular processes such as replication and transcription. Recently, it has been shown that especially the presence of G-quadruplexes in DNA is important for regulation in the cell, but also for the regulation of the life cycle of various viruses (HIV, HSV, EBV). These local structures are recognized by a variety of proteins. As part of this dissertation, the occurrence of non-canonical structures in genomes will be studied with a focus on cross structures and quadruplex DNA and their occurrence in genes with the potential for medical use. Bioinformatic, physical, biochemical and molecular biological methods will be used to study the recognition of target structural motifs in the promoter region of genes. Microscopic methods, including confocal microscopy, will also be used to study localization and interactions in cellular systems. Cooperation with a foreign workplace is assumed.

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

3. 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.

4. Diagnostics and application of non-thermal plasma in decontamination processes

   Nowadays, the global research is focused on as low application of chemicals and antibiotics in sterilization of both living and inanimate materials as possible. The application of low temperature plasma seems to be a suitable alternative to conventionally used means because it gently affects treated materials and does not produce higher amount of side pollutants. Therefore, the thesis will be focused on the assessment of low temperature plasma suitability for decontamination of solid and liquid surfaces and media. The low temperature plasma will be generated by different electrical discharges. Besides diagnostic methods for plasma characterization, various biological, chemical and material analyses will be employed in order to understand initiated processes.

   Tutor: Kozáková Zdenka, doc. Ing., Ph.D.

5. 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.

6. Hydrogels with fibrous structures

   Hydrogels represent a versatile platform for a variety of biomedical applications – for example, in the drug delivery, as extracellular matrix models, or in tissue engineering. They mimic real biological environment like tissues or extracellular matrix. Such biological environments are essentially formed by a network skeleton in which fibrous structures are embedded. PhD study will start with a sufficiently thorough literature search and then will focus on preparation of hydrogels with incorporated fibrous structures and on investigation of the influence of the fibers on the properties of resulting hydrogels. Both constituents of the final composite will be selected from two biopolymer groups – polysaccharides and proteins. The effect of the fibrous structures on the properties of hydrogels, which are important for their potential applications in the field of biomedicine and drug delivery, will be studied in detail. Particularly rheological and transport properties will be addressed. Results will be discussed from the viewpoint of preparing hydrogels with properties tailored to a specific medical application and should lead to formulation of concrete composition and preparation procedure of a material suitable for a given application.

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

7. Hydrogels with fibrous structures

   Hydrogels represent a versatile platform for a variety of biomedical applications – for example, in the drug delivery, as extracellular matrix models, or in tissue engineering. They mimic real biological environment like tissues or extracellular matrix. Such biological environments are essentially formed by a network skeleton in which fibrous structures are embedded. PhD study will start with a sufficiently thorough literature search and then will focus on preparation of hydrogels with incorporated fibrous structures and on investigation of the influence of the fibers on the properties of resulting hydrogels. Both constituents of the final composite will be selected from two biopolymer groups – polysaccharides and proteins. The effect of the fibrous structures on the properties of hydrogels, which are important for their potential applications in the field of biomedicine and drug delivery, will be studied in detail. Particularly rheological and transport properties will be addressed. Results will be discussed from the viewpoint of preparing hydrogels with properties tailored to a specific medical application and should lead to formulation of concrete composition and preparation procedure of a material suitable for a given application.

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

8. Hydrogels with fibrous structures

   Hydrogels represent a versatile platform for a variety of biomedical applications – for example, in the drug delivery, as extracellular matrix models, or in tissue engineering. They mimic real biological environment like tissues or extracellular matrix. Such biological environments are essentially formed by a network skeleton in which fibrous structures are embedded. PhD study will start with a sufficiently thorough literature search and then will focus on preparation of hydrogels with incorporated fibrous structures and on investigation of the influence of the fibers on the properties of resulting hydrogels. Both constituents of the final composite will be selected from two biopolymer groups – polysaccharides and proteins. The effect of the fibrous structures on the properties of hydrogels, which are important for their potential applications in the field of biomedicine and drug delivery, will be studied in detail. Particularly rheological and transport properties will be addressed. Results will be discussed from the viewpoint of preparing hydrogels with properties tailored to a specific medical application and should lead to formulation of concrete composition and preparation procedure of a material suitable for a given application.

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

9. Hydrogels with fibrous structures

   Hydrogels represent a versatile platform for a variety of biomedical applications – for example, in the drug delivery, as extracellular matrix models, or in tissue engineering. They mimic real biological environment like tissues or extracellular matrix. Such biological environments are essentially formed by a network skeleton in which fibrous structures are embedded. PhD study will start with a sufficiently thorough literature search and then will focus on preparation of hydrogels with incorporated fibrous structures and on investigation of the influence of the fibers on the properties of resulting hydrogels. Both constituents of the final composite will be selected from two biopolymer groups – polysaccharides and proteins. The effect of the fibrous structures on the properties of hydrogels, which are important for their potential applications in the field of biomedicine and drug delivery, will be studied in detail. Particularly rheological and transport properties will be addressed. Results will be discussed from the viewpoint of preparing hydrogels with properties tailored to a specific medical application and should lead to formulation of concrete composition and preparation procedure of a material suitable for a given application.

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

10. Novel plasma systems for therapeutic applications

    Applications of low temperature atmospheric pressure plasmas in medicine are one of the current hot topics in plasma sciences. Various plasma systems were developed recently mainly for sterilization, blade coagulation or acceleration of wound healing. The specific research is focused on selected wounds where current classical therapies are failing as well on oncology. There is still a great demand of new simple and cheap plasma systems that can be applicable for these applications. The PhD study will be focused mainly of characterization of novel plasma systems with respect to their applicability in direct interaction with living tissue. The main characteristics are temperature of the treated surface and presence of various active particles like radicals and photons. Properties of new systems constructed by supervisor and his colleagues from abroad will be characterized by fast camera imaging, optical emission spectrometry and Fourier transform infrared spectrometry. The flow visualization will be examined by Schlieren photography under cooperation with Bologna University in Italy. The systems efficiency will be also tested in vitro using selected non-pathogenic microorganisms.

    Tutor: Krčma František, prof. RNDr., Ph.D.

11. Preparation and study of vesicular complexes with polymers

    This work is focused on the preparation and study of vesicular systems that, by their structure, surface charge and other properties, will be suitable for interaction with charged or uncharged polymers and together will form a water-soluble biocompatible complex that will be stable under physiological conditions. The study envisages the use of stationary, time-resolved and microscopic fluorescence techniques together with other available techniques such as dynamic light scattering, atomic force microscopy, chromatographic methods, etc. As part of the study, in-depth knowledge of fluorescence techniques and procedures for the preparation of colloidal complexes will be acquired.

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

12. Protein-DNA interactions with a focus on proteins important in oncology

    The interaction of proteins with nucleic acids plays a fundamental role in biological systems. A number of proteins bind sequence-specifically, and other proteins bind to different local structures in DNA. Recently, it has been shown that especially the presence of cross structures and G-quadruplexes in DNA is important for regulation in the cell, but also for the regulation of the life cycle of various viruses. G-quadruplexes are also very often found in the promoters of human oncogenes and are therefore considered as suitable targets for antitumor therapy. In the framework of this dissertation, the interaction of proteins with local DNA structures will be studied, with a focus on cross-linked structures and quadruplex DNA. Bioinformatic, physical, biochemical and molecular biological methods will be used, including the yeast isogenic system for studying the recognition of non-canonical structures and their interaction with nucleic acids. Microscopic methods will also be used to study localization and interactions in cellular systems. Cooperation with a foreign workplace is assumed.

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

13. Self-entrapment of Plant Growth Promoting Rhizobacteria by gelation of their exopolysaccharides – towards the next-generation bioinoculants

    Encapsulation of Plant Growth Promoting Rhizobacteria (PGPR) in hydrogel carriers represents state-of-the-art in production of agricultural bioinoculants that are used to restore soil fertility and to enhance the yield of crops. The hydrogel matrix enhances bioinoculant performance by protecting the cells against various environmental stress factors that accompany its application, however, the encapsulation step provided by addition of an external gelation component reduces the economic feasibility of the bioinoculant production. We have proposed a novel concept of biofertilizers based on the entrapment of PGPR (from the genus Azotobacter) in the gel formed from alginate produced directly by the employed bacteria. The PhD project will focus on in-depth study of selective essential steps – PGPR cultivation, gelation and drying of the bioinocullants and/or pilot screening of their bioactivity. The essential fundamental knowledge will be gained on the causal relationship between preparation procedure, structure and crucial properties of the bioinocullants based on this original strategy.

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

14. Self-entrapment of Plant Growth Promoting Rhizobacteria by gelation of their exopolysaccharides – towards the next-generation bioinoculants

    Encapsulation of Plant Growth Promoting Rhizobacteria (PGPR) in hydrogel carriers represents state-of-the-art in production of agricultural bioinoculants that are used to restore soil fertility and to enhance the yield of crops. The hydrogel matrix enhances bioinoculant performance by protecting the cells against various environmental stress factors that accompany its application, however, the encapsulation step provided by addition of an external gelation component reduces the economic feasibility of the bioinoculant production. We have proposed a novel concept of biofertilizers based on the entrapment of PGPR (from the genus Azotobacter) in the gel formed from alginate produced directly by the employed bacteria. The PhD project will focus on in-depth study of selective essential steps – PGPR cultivation, gelation and drying of the bioinocullants and/or pilot screening of their bioactivity. The essential fundamental knowledge will be gained on the causal relationship between preparation procedure, structure and crucial properties of the bioinocullants based on this original strategy.

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

15. Study of plasma interaction with soil environment

    The recent research focusing on non-thermal plasma application in agriculture is aimed mostly on the influence of direct plasma effects or indirect effects of plasma activated water on plant materials. However, effects on the soil environment are still less examined, both from the physical-chemical and microbiological point of view. Therefore, the thesis will be focused on the study of both direct and indirect low temperature plasma interaction with the soil environment. The low temperature plasma will be generated by different electrical discharges. The goal of the work will be a description of plasma effects on the soil physical-chemical properties as well as on the soil microorganisms. Besides methods for plasma diagnostics, various biological and chemical analyses will be employed for the study.

    Tutor: Kozáková Zdenka, doc. Ing., Ph.D.