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 DNA binding proteins with a focus on their interaction with local DNA structures

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

3. Bio-applications of plasma activated water

   By the interaction of plasma with water, so-called plasma activated water is produced that has different physical properties as well as chemical composition. These changes are caused mainly by the production of oxygen and nitrogen reactive species, in the dependence on the plasma activated water preparation. Thanks to its high oxidation and sterilisation potential, plasma activated water is a contemporary hot topic both in biomedicine and agriculture. Due to the enhanced amount of nitrogen species, it can also serve as an alternative method of fertilisation. The work itself will deal with plasma activated water applications on selected microorganisms and fungi in order to evaluated efficiency of this medium in human and veterinary medicine or agriculture.

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

4. 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.).

   Tutor: Obruča Stanislav, prof. Ing., Ph.D.

5. 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.).

   Tutor: Obruča Stanislav, prof. Ing., Ph.D.

6. Controlled release from hydrogels

   Hydrogels still represent an attractive material in the formulating systems for the controlled release of biologically active substances. These are applied not only in medicine or food engineering but also, for example, in agriculture. Despite of the huge number of experimental works and of the knowledge of theoretical background of the release, the design and development of controlled delivery systems is still more matter of trial and error than of rational design rules. Even the very controlled release in real applications is not covered by clear procedures. The thesis will thus focus on the generalization of published knowledge on the controlled release from hydrogel matrices, supported by student’s experimental work and modelling the release in particular with regard to in vivo conditions. Following the initial literature search partial tasks will be formulated including (all or selected) issues like: • laboratory test studies of the release, influence of their parameters on the results, rational standardization of experimental protocols, • diffusivity of the selected (model) drug as a function of the hydrogel or gelator concentration, • transport and interaction of the selected (model) drug in different hydrogel systems, relation to problems observed in real applications; influence of conditions found in real environments (e.g., pH, temperature), • modelling of drug release profiles with experimentally determined parameters and with regard to release and transport in real matrices (tissues). The thesis will result in suggestion of a set of rational rules to select a suitable hydrogel for the encapsulation and controlled release of a given molecule in a particular environment.

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

7. Direct plasma application for therapeutic purposes

   Thesis will be focused on the direct therapeutic application of low temperature non-equilibrium plasma for sterilization and wound healing. There are expected mainly in vitro experiments, in vitro as well as in vivo experimeents with pathogens are planned under collaboration with Veterinary University

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

8. 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.

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

9. Mobility of hormones and drugs in hydrogel systems

   On the basis of literature search, drugs and hormones (potentially harmful in natural systems). Their transport in hydrogels containing humic substances as active substances which play key role in interactions with pollutants and their immobilization in nature will be studied.

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

10. 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.

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

11. Nanotechnology and microtechnology for analysis of complex samples by Raman spectroscopy

    Raman microspectroscopy provides information about the molecular composition of the sample under investigation. In recent years, Raman spectroscopy has been used to identify microorganisms, because each microorganism has a unique Raman spectrum (the so-called "fingerprint"). Contemporary microtechnologies and nanotechnologies include a number of unique tools and procedures. These allow amplification of the Raman signal, for example from the surface of bacteria, through nanostructures made of noble metals (so-called SERS), spatial localization of microobjects (including living cells) in a light beam (so-called optical tweezers) and sterile separation of microobjects or components of suspensions, surface arrangement of microparticles and their transport (microfluidic systems). The main goal of the doctoral dissertation thesis will be to combine the above techniques so that it is possible to use Raman microspectroscopy to study the molecular composition of individual microorganisms (bacteria and eukaryotic cells) suspended in a liquid medium and monitor the responses of microorganisms to defined external stimuli or stress factors. It is assumed that the doctoral student will be able to operate and modify the experimental system implemented in the Institute of Scientific Instruments of the Academy of Sciences of the Czech Republic, v.v.i. In particular, the amplification of the intensity of Raman scattering spectra near metal micro- and nano-structures will be investigated by the SERS - Surface Enhanced Raman Spectroscopy technique, realized in microfluidic chips. The procedures found and the results obtained will significantly contribute to the rapid identification of microorganisms and the evaluation of their response to stressors, including antibacterial drugs. The dissertation assumes experimental and theoretical activities at the Institute of Instrumentation of the ASCR, v.v.i., which will provide all the necessary equipment. The department cooperates with a number of European laboratories dealing with related issues, which offers applicants the opportunity for internships abroad and rapid professional growth.

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

12. Preparation and characterisation of biocomposites based on lignocellulosic wastes

    The main idea of PhD. Research on this topic is the processing of lignocellulosic waste materials from the perspective of circular economics. This means first isolating all valuable substances from lignocellulosic materials, characterising them and using them purposefully. The main goal will be to prepare biocomposites with good mechanical properties, which will have functional surfaces with properties suitable for use in various fields of medicine and pharmacy. The main principle of this work is based on the processing and characterisation of biocomposite materials based on polyesters (polylactide, polyhydroxyalkanoates or polycaprolactone), cellulose nanocrystals (derived from bacterial cellulose or plant cellulose) and phenolic compounds. The important tasks of the research work will be to achieve good interfacial compatibility between the polymer matrix and additives and, at the same time to support the antibacterial activity of biocomposites and finally suggest complete processing of selected waste material into valuable chemicals and products in a sustainable way.

    Tutor: Kovalčík Adriána, prof. Ing., Ph.D.