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Department of Biotechnology

List of available PhD theses

Application of non-traditional microorganisms for the production of fermented beverages

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie

Annotation

The brewing industry and the entire fermented beverage industry have recently experienced rapid development in the area of new trends in the use of non-traditional microorganisms. The aim of the work will be to identify and test various microorganisms for use in the production of beer, ciders, and other fermented beverages and determine their characteristics.

Biologically active substances in hops; their effects and uses

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie

Annotation

In the Czech Republic, some hops varieties have been bred for non-brewing purposes, mainly pharmaceutical. These varieties have high contents of prenylflavonoids (xanthohumol and desmethylxanthohumol). Desmethylxanthohumol is a precursor of 8-prenylnaringenin, which is the strongest known phytoestrogen. Demethylation of isoxanthohumol can also yield extracts with high levels of 8-prenylnaringenin. The goal of this work will be to determine the concentration of these substances in hops, test their biological effects, and develop methods for preparing extracts with enhanced levels of these substances for use as food supplements.

Capsid lattice formation of RNA viruses

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie
Theses supervisor: doc. Dr. Ing. Michaela Rumlová

Characterization and use of newly developed biodegradable and recyclable polymeric materials in biotechnology and other fields

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie

Annotation

The research is carried out in cooperation with Institute of Macromolecular Chemistry of the AS CR, v.v.i., Prague, that designs advanced polyurethane materials with adjustable biodegradation rate. Polyurethanes are synthesized as polyester-ether polyols with different ether/ester segment ratios to achieve specific polymer structure density and suitable surface properties (hydrophobicity, charge) to improve microorganism adhesion and hydrolytic degradability. Research includes evaluation of individual polymeric materials in the context of intended use (e.g. as biofilm carrier in packed reactors, biodegradable fillers for product packaging, filaments for 3D printing) and analytical evaluation of four basic processes of biological action on polyurethane material: structural disruption (FTIR and Raman spectroscopy SEM), fragmentation (MALDI-TOF, HPLC-UV/RI, HPLC-MS and GC-MS), assimilation (Oxitop) and surface colonization (zeta potential, contact angle and image analysis). In case of interest, it is also possible to participate in the research of polymer synthesis at the Institute of Macromolecular Chemistry, thus, to set dissertation thesis as multidisciplinary.

Enzymes and biologically active molecules as effective components of biopesticides

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie

Annotation

In order to replace synthetic pesticides, recently, biopesticides based on enzymes and/or secondary metabolites of microorganisms have come to the forefront. Biopesticides are one of the main pillars of modern environmentally oriented approaches in (intensive) agriculture based on the prevention of environmental pollution. Such an environmentally friendly product should be designed as a mixture of biologically active molecules, thanks to which it has unique properties and complex effect. The genus Pseudomonas (e.g. Pseudomonas gessardii) appears to be a promising producer of biologically active molecules based on enzymes (chitinolytic enzymes), antibiological agents (pigments) or adjuvants (siderophores). From a technological point of view, the genus is a suitable producer that does not require demanding cultivation processes and expensive cultivation media. The research includes screening of suitable producers, comprehensive description of their properties and production of promising substances and design of suitable cultivation methods and bioreactors to produce active components of biopesticides.

Epiphytic and endophytic microorganisms of hops and their biotechnological potential

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie
Theses supervisor: prof. Dr. Ing. Petra Patáková

Annotation

The work will focus on the isolation and identification of microorganisms from various parts of the hop plant and on further investigation of selected isolates. Attention will be focused on the search for bioactive substances that could be used as growth stimulators or inhibitors of fungal growth in hop growing. Furthermore, the influence of selected isolates on hop storage and beer production will be monitored. The outputs of the work will be directed to both basic research (microflora mapping) and the application sphere (development of bio-spraying for plants based on plant probiotics). Various methods will be used in the work, from classical culture microbiological techniques, through MALDI and 16SrRNA identification of isolates (in selected cases, possibly sequencing of the whole genome in the case of bacteria) to various chromatographic techniques and methods of testing biological activity.

Fermentation production of bio-hydrogen using clostridia

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie
Theses supervisor: prof. Dr. Ing. Petra Patáková

Annotation

Hydrogen offers various uses, in direct combustion without the formation of CO2, as a reducing agent for chemical reactions or as one of the precursors of methane production. The work will focus on the study of hydrogen production in Clostridial fermentation using both pure cultures and consortia of microorganisms. The outputs of the work will be directed both to basic research (study of hydrogenases and finding the exact mechanism of hydrogen production in Clostridium beijerinckii) and to the application sphere (utilization of various types of waste for hydrogen production and other metabolites, which will then be led to the biogas plant and used to strengthen methanation ). The work assumes routine mastery of various techniques, such as bioreactor cultivation, analysis of gaseous and liquid metabolites, study of gene transcription using RT-qPCR techniques, microscopy and others.

Functional,- structural characterization of the NMDA receptor channel

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie
Theses supervisor: doc. Dr. Ing. Michaela Rumlová

Annotation

N-methyl-D-aspartate (NMDA) receptors are a type of ionotropic glutamate receptors mediating fast synaptic transmission and are essential for learning and memory. Abnormal function of NMDA receptors underlies many neurological and psychiatric diseases, including schizophrenia and neurodegenerative disorders. We use advanced electrophysiology, molecular biology, optogenetics, and microscopy to investigate the relationship between the structure and the function of NMDA receptor ion channels, to characterize molecular mechanisms of action of different pharmacological agents influencing them, and to study the physiological and pathological processes in which NMDA receptors participate. The aim of the PhD project is to characterize functional consequences of de-novo and other mutations found in individuals diagnosed with schizophrenia, mental retardation, autism, or epilepsy for the function of the NMDA receptor and to rectify impaired function by newly synthetized steroid compounds. Disease-associated mutations will be studied in recombinant NMDA receptors expressed in HEK cells and native receptors in cultured hippocampal neurons derived from GMO mice. The project will include the characterization of consequences of mutations for synaptic transmission and behavior, both under normal conditions and in mouse and zebrafish models of neurological and psychiatric disorders. Cultured hippocampal neuron; negative and positive allosteric effect of neurosteroids; structure of NMDA receptor.

Manifestations of synergy and antagonism in multispecies biofilms

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie
Theses supervisor: prof. Ing. Jan Masák, CSc.

Annotation

Biofilm formation and other virulence factors are subject to different regulatory mechanisms which, depending on the particular microorganism, use different types of chemical compounds as regulatory signales. In multispecies biofilms, a complex system of these molecules is created. They can enter into interactions with each other or with the microorganisms present and significantly influence the mentioned regulatory mechanisms, which then result in very different relationships throughout the microbial community. The subject of the proposed dissertation topic is the targeted formation of multispecies communities and understanding of their physiology and other properties during the formation and stabilization of biofilm.

New possibilities for prediction of beer colloidal stability

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie

Annotation

One of the limiting factors of beer stability is its colloidal stability. The colloidal stability of beer is determined by the composition of the colloidal system of beer and is influenced by other factors. The aim of this work is to find such methods of characterization of the colloidal system of beer that would allow us to predict its colloidal stability during the time. Another aim of the work is to find the reasons for reduced colloidal stability in different kinds of beers.

Non-Traditional Yeasts with Potential to Produce Special Fermented Beverages

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology

Annotation

Today's beer market is very diverse and all producers are looking for ways to differentiate themselves. The aim of this work will be to find such yeasts that could be used for fermentation and at the same time provide an interesting and unique aroma of the final product in comparison with normal fermented beer. A secondary goal will be the search for a strain of microorganisms usable for the production of non-alcoholic beer.

Production of alcohol-free beer in the conditions of a mini-brewery

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnology

Annotation

Currently, two trends are recognizable in brewing. The first is the rapid development of microbreweries. The second trend is the increasing production of non-alcoholic beers, which are not yet produced in mini-breweries. The aim of the work is to research and development of technology for the production of non-alcoholic beers in mini-breweries.

Reactors for in-vitro organs (Bioengineering of in-vitro organs)

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programmes: Biotechnologie, Biotechnology
Theses supervisor: Ing. Gabriela Kuncová, CSc.

Annotation

Currently, vast failures of organs, such as liver, lungs, kidney, or the heart might be treated only by a transplantation. Due to critical shortage of donor organs great research attention has been focused to tissue engineering, which employs elements including cells, scaffolds, and growth factors to fabricate functional organs in vitro. As scaffolds have been used both, decellurized organs and artificial porous materials. The aim of the project is a research of reactors for in-vitro cell seeding and cultivation of scaffolds. The study will be done in cooperation with institutions preparing natural and artificial scaffolds, Biomedical Center of Faculty of Medicine of Charles University in Pilsen and Institute of Macromolecular Chemistry of the Czech Academy of Sciences. Experimental work will comprise a study of permeability of scaffolds using non-living particles, and design and verification of functionality of reactors. Required education and skills • Master degree in biotechnology, chemical engineering, physical chemistry, biomedical engineering; • Positive attitude to experimental work in laboratory; • An ability for interdisciplinary cooperation.

Structural and functional diversity of bioactive specialized metabolites produced by Actinobacteria

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie
Theses supervisor: prof. Ing. Jan Masák, CSc.

Annotation

Actinobacteria represent a renowned source of a broad spectrum of biologically active metabolites applicable in medicine. Even though this source of natural products nowadays faces challenges such as re-discovery of known compounds, we assume that we may exploit the once efficient source of antibiotics or anticancer drugs again if we employ more innovative strategies. Within this project, we will prepare a library of extracts and fractions containing metabolites obtained from a collection of soil Actinobacteria. We will attempt to target the compounds of interest in the upstream workflow process using modern metabolomics approaches. We will screen the library against a set of multi-drug resistant pathogens, for which antibioticas are urgently needed according to the World Health Organisation. These include Clostridioides (Clostridium) difficile, Staphylococcus aureus, Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and others. We will also submit samples with the metabolites from Actinobacteria into the chemical library of the CZ-OPENSCREEN facility for high throughput screening of various specific biological activities. The most promising metabolites will be purified and structurally elucidated by mass spectrometry and nuclear magnetic resonance.

Study of the use of biocontrol agents against fungal biofilms

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Mikrobiologie

Annotation

The subject of this doctoral project is to investigate the methods of application and effectiveness of biocontrol agents (eg Pythium oligandrum, Geotrichum candidum) against fungal biofilms (eg genera Aspergillus, Penicillium and Fusarium) and the experimental study of factors (physicochemical, nutritional, culture, hydrodynamic) that affect it. The experiments will be performed in various configurations (static, dynamic) using experimental design and evaluation by statistical methods. The project also aims to compare experimental data on the effectiveness of biofungicide with model prediction of its adhesion to fungal biofilms and model surfaces (X/DLVO theory, interfacial free energy balance) based on physicochemical surfaces properties. Using the agreement between experiments and models, the controlling force of biofungicide interaction with biofilm can be identified. In the case of interaction of biofungicide cells with model surfaces, the conditions under which they can be preventively treated with a biofungicide will be defined. All successful attempts to remove/suppress fungal biofilm with biofungicide will be accompanied by a quantitative determination of mycotoxins.

The benefit of 4-alkyl-L-proline motif for biological activity of microbial metabolites with distinct modes of action

Department: Department of Biotechnology, Faculty of Food and Biochemical Technology
Study programme: Biotechnologie
Theses supervisor: prof. Ing. Jan Masák, CSc.

Annotation

4-Alkyl-L-proline derivatives with a two- or three- carbon side chain represent rare building blocks of metabolites produced by Actinobacteria. Only five groups of compounds with remarkably distinct biological activities share this structural motif. The metabolites cover antimicrobial compounds with different spectrum of targeted microorganisms as well as metabolites with various antitumor effects. The modes of action of these metabolites are also diverse – they include interaction with bacterial ribosome (lincomycin), binding to the minor groove of DNA (pyrrolobenzodiazepines), and inhibition of bacterial enzymes participating in DNA synthesis (mycoplanecin). Target biological structures of the two remaining groups of compounds (hormaomycin, lucentamycin) are still elusive. Whereas the positive effect of the 4-alkyl side chain on the biological activity was well documented for lincomycin, the significance of this evolutionary and biosynthetically complex structural motif for the activity of the remaining metabolites is not clear. Within this project, we will prepare metabolites with incorporated 4-alkyl-L-proline derivative and their analogues with common L-proline and compare their relevant biological activity. The metabolites will be mostly isolated from the culture broth of producing strains including the use of semi-synthetic approaches (eg. precursor-directed biosynthesis or mutasynthesis) and modern analytical chemistry approaches. The project objective will be to evaluate the general benefit of the 4-alkyl-L-poline motif for the level of various biological activities. The new knowledge obtained may be exploited for the biotechnological preparation of efficient compounds potentially applicable in medicine.


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