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PhD topics for academic year 2021/2022

Department of Biochemistry and Microbiology

Faculty of Food and Biochemical Technology

Analysis of multispecies biofilms of food-borne pathogenic bacteria

Demnerová Kateřina, prof. Ing. CSc. ( dem...@vscht.cz)
Zdeňková Kamila, Ing. Ph.D. ( zde...@vscht.cz)
Most bacteria, due to their phenotypic adaptability, can live in a community called biofilm, which is often multi-species. Biofilm serves for their adherence, communication, protection and increases the resistance of bacteria to adverse environmental conditions. Its characteristic persistence, heterogeneity and complex dynamics are related to relatively difficult detection and problematic analyses by classical microbial methods. That is why such consortia are nowadays a challenge for many professionals. Multi-species biofilms of Listeria monocytogenes, Staphylococcus aureus and Escherichia coli, will be analysed during the course of the dissertation as selected representatives of food pathogens monitored under Commission Regulation (EC) 2073/2005. Classical microbiological and modern molecular-biological methods will be used. The multi-species biofilm study will also include analyses of gene expression levels and impact on biofilms of antibiotics or other selected antimicrobials. This will contribute to a better understanding of the spread of resistance in the environment assisted by these communities, while at the same time increasing the existing knowledge about the coexistence of the biofilms of bacteria whose eradication from undesirable sites is more complicated than single-species biofilms.
Faculty of Food and Biochemical Technology

Anammox bacteria and their unique phospholipids

Lipovová Petra, doc. Ing. Ph.D. ( kar...@vscht.cz)
Anammox (anaerobic ammonium oxidation) bacteria, which were discovered relatively recently, play an important role in the global nitrogen cycle, thanks to their unique metabolism, the conversion of ammonium cation (NH4+) and nitrite (NO2-) to nitrogen. In this way, up to 50 % of ocean nitrogen is produced in oxygen-restricted zones. Currently, these microorganisms are used in wastewater treatment as ideal substitutes for the denitrification process. The sequence of reactions of anammox metabolism takes place on the membrane of a special compartment inside these bacteria called the anammoxosome. All membranes of anammox bacteria, including the anammoxosome, are composed of unique ladderan lipids. These are phospholipids which contained 5 cyclobutanes or a combination of 3 cyclobutanes with cyclohexane at the end of the acyl chain. Thanks to these unique lipids, the membrane of the anammoxosome transmits protons up to ten times slower than the classical bilayer of phospholipids, which helps maintain the proton-motive power of these bacteria. Not much is known about the synthesis of these special phospholipids. The aim of this work will be to contribute to the detection of enzymes involved in the synthesis and degradation of these phospholipids in anammox bacteria.
Faculty of Food and Biochemical Technology

Bacterial L-asparaginases with therapeutical and biotechnological potential

Lipovová Petra, doc. Ing. Ph.D. ( kar...@vscht.cz)
Benešová Eva, Ing. Ph.D. ( Eva...@vscht.cz)
L-Asparaginases belong to enzymes with therapeutical and biotechnological potential. They are used in the treatment of acute lymphoblastic leukemia and also for the reduction of the content of toxic acrylamide in food. The antitumor activity of L-asparagineses results from the fact that some tumor cells are unable to synthesize L-asparagine and must therefore receive it from their environment. The effective reduction of its concentration in their surroundings by the action of L-asparaginases therefore results in the termination of preteosynthesis and other related processes and finelly in the death of tumor cells. L-Asparaginases originating from Escherichia coli and Dickeya dadantii are currently used in the clinical practice. However, their application is accompanied by a number of side effects, and for this reason there is an effort to find new enzymes suitable for clinical use and with minimal side effects. The aim of this work is therefore to identify new bacterial producers of L-asparaginases with suitable characteristics for therapeutic use. Particular attention will be paid to organisms whose enzyme equipment has not yet been characterized in detail, such as marine or cold-adapted bacteria.
Faculty of Food and Biochemical Technology

Fish identification: molecular-biological and proteomic approaches

Demnerová Kateřina, prof. Ing. CSc. ( dem...@vscht.cz)
Zdeňková Kamila, Ing. Ph.D. ( zde...@vscht.cz)
Food market is still broadened with new products from different producers and suppliers, which increases the diversity of consumers' menus on one hand, but therewithal it creates conditions for food fraud on the other hand. Food fraud may be associated also with health hazards for consumers. The consumers´ misleading can be done e.g. by replacing more expensive raw materials with cheaper ones, failing in complying the declared composition or by deliberately mislabelling the geographical origin or the production method. One category of often-falsified food are fish, fish products and seafood, which are also associated with the occurrence of significant allergens. The work aims to develop and experimentally verify methodologies for the identification of fish using DNA and protein analysis. Molecular-biological methods should allow such species determination within the class of Actinopterygii, and will comprise modern methods such as polymerase chain reaction (PCR, qPCR, and dPCR) and sequencing. The target gene to be analysed is the gene encoding the main fish allergen, parvalbumin. The proteins analysis will be aimed at comparing proteins profiles obtained by mass spectrometry MALDI-TOF.
Faculty of Food and Biochemical Technology

Cutibacterium acnes: virulence factors and mobile genetic elements

Zdeňková Kamila, Ing. Ph.D. ( zde...@vscht.cz)
The gram-positive bacterium Cutibacterium acnes (formerly Propionibacterium acnes) is a skin commensal under physiological conditions, but it can also be an opportunistic pathogen causing invasive chronic infections. The most well-known diseases associated with C. acnes include Acne vulgaris; however, the connection with a number of other diseases is also clinically significant. The pathogenicity of C. acnes is due to a number of virulence factors, one of which is the formation of a biofilm, which increases the resistance of bacteria to antibiotics and other bactericidal substances, which negatively affects the effectiveness of treatment. C. acnes phylotype IA1, associated with acne, produce virulence factors as hemolysins, CAMP factors, neuraminidase, heat shock proteins (HSP) or lipase etc. Much of genes responsible for virulence and resistance is located on mobile genetic elements (MGEs). As part of the solution of this work, virulence factors will be studied using classical microbiological and modern molecular-biological methods.
Faculty of Food and Biochemical Technology

Impact of antibiotic resistance on the propagation of Gram-negative bacteria in the food chain

Purkrtová Sabina, Ing. Ph.D. ( pur...@vscht.cz)
The increasing incidence of antibiotic resistance in bacteria is one of the major problems of the 21st century, as it limits the range of suitable antibiotics for treating bacterial infections. The food chain is one of the places, where it happens the genesis of new antibiotics resistance determinants and/or their spreading (so-called hot spots). Selected groups of gram-negative bacteria (family Enterobacteriaceae, the genera Acinetobacter and Pseudomonas, etc.) form the very significant or the most numerous parts of bacteriome in many food products. At the same time, these bacterial groups are frequent carriers and spreaders of antibiotic resistance genes (e.g. by various mechanisms of horizontal gene transfer). However, the presence of antibiotic resistance genes, often linked to various mobile genetic elements, can not only bring benefits to their carriers, but in some cases can have a negative effect on their certain physiological and other properties (eg growth ability). Knowledge of the influence of the presence of antibiotic resistance genes on properties important for the spread of bacteria in the food chain (e.g. biofilm formation, growth ability, resistance to environmental stress conditions, etc.) is then important for determining the potential for their spread in the food chain and for developing methods to reduce it. The aim of the work will be to study and compare the isolates of the above groups of gram-negative bacteria isolated from food products with different antibiotic resistance profiles. The selection of important antibiotic resistance genes occurring in food isolates of the above groups of gram-negative bacteria will be performed. Furthermore, the occurrence of these antibiotic resistance genes in selected food products will be determined. It will be performed the isolation and quantification of target bacterial groups, genotypic and phenotypic characterization of the obtained isolates and comparison of the occurrence frequency of different genotypes and phenotypes. Modern methodological approaches such as next generation sequencing methods (e.g. nanopore sequencing), qPCR, MALDI-TOF MS and selected classical cultivation microbiological methods will be used for the study.
Faculty of Food and Biochemical Technology

Isolation of novel therapeutics form fungi

Kotrba Pavel, prof. Ing. Ph.D. ( kot...@vscht.cz)
Kuchař Martin, doc. Ing. Ph.D. ( mar...@vscht.cz)
Fungi have been always on the forefront of biotechnological research, be it for antibiotics, food production, various enzymatic mixtures etc. Yet, there is still an untapped potential with regards to therapeutic use against cancer or various psychological disorders, although there are reports of fungi being traditionally used for such purposes. This dissertation project is aimed on the identification and isolation of novel therapeutics from common forest fungi such as Amanita muscaria and testing of the therapeutic potential of the isolated substances in various types of cancer cell lines.
Faculty of Food and Biochemical Technology

Mechanisms of bacterial antibiotic resistance and their modulation

Viktorová Jitka, Ing. Ph.D. ( pro...@vscht.cz)
Faculty of Food and Biochemical Technology

Microbial Cometabolism: Promoting Biodegradation of Pollutants

Uhlík Ondřej, doc. Ing. Ph.D. ( Ond...@vscht.cz)
Strejček Michal, Ing. Ph.D. ( str...@vscht.cz)
The objective of the proposed thesis is to test the hypothesis that secondary plant metabolites can promote cometabolism of persistent organic pollutants in the environment and thereby significantly influence the biodegradation potential of autochthonous microbial communities. In order to accomplish this objective, we will (i) selectively enrich soil bacterial consortia that will degrade selected pollutants (polychlorinated biphenyls, PCBs, and polyaromatic hydrocarbons, PAHs) when grown on secondary plant metabolites and (ii) test whether the consortia involved in secondary plant metabolite metabolism will increase the efficiency of biodegradation of PCBs and PAHs in soils.
Faculty of Food and Biochemical Technology

Microbiota of Selected Extreme Biotopes – Diversity, Ecology and Physiology

Uhlík Ondřej, doc. Ing. Ph.D. ( Ond...@vscht.cz)
Šuman Jáchym, Ing. Ph.D. ( sum...@vscht.cz)
The objective of the proposed thesis is to characterize microbial populations in extreme biotopes – chronosequence of permafrost (permafrost of differing age) and soils from salt marshes and moffettes. The characterization will be conducted by two major routes – metagenomics and modified cultivation techniques. The basic modification of the cultivation techniques will be the use of resuscitation-promoting factor and adjustment of cultivation media so that they better mimic natural conditions the bacteria are subjected to in their habitat; the goal is to increase the efficiency of the cultivation and isolate dormant or otherwise difficult-to-culture or, if possible, as-yet-uncultured bacteria.
Faculty of Food and Biochemical Technology

Microorganisms and their utilisation in waste management

Stiborová Hana, Ing. Ph.D. ( han...@vscht.cz)
Nowadays, more attention is paid to recycling and recovery of waste and therefore, the European Union has adopted a new Circular economy action plan. One option of reducing the environmental burden and decreasing the CO2 emissions in the (cement) building industry is the usage of recycled bio-concrete, which can be obtained using microbiologically induced calcite precipitation (MICP). This thesis's main goal will be to isolate and characterise suitable microorganisms and optimise MICP conditions concerning the yields, the structure and mechanical properties of bio-concrete.
Faculty of Food and Biochemical Technology

Novel approaches in the elimination of cancer cells and bacterial biofilms

Zelenka Jaroslav, doc. Ing. Ph.D. ( ZEL...@vscht.cz)
Faculty of Food and Biochemical Technology

Preparation and structural-functional analysis of virus-like and non-viral nanoparticles

Ruml Tomáš, prof. Ing. CSc. ( r...@vscht.cz)
Častorálová Markéta, Ing. Ph.D. ( Mar...@vscht.cz)
The work is focused on the preparation of nanoparticles by self-assembly of viral structural proteins and on the basis of modified organic and inorganic structures. The particles will be surface modified to target pathogenic bacteria or tumor cells. Their ability to interact with target organisms for use in inhibiting, imaging and modulating cellular activity will be evaluated.
Faculty of Food and Biochemical Technology

Quorum sensing and its role in adaptation and virulence of Campylobacter jejuni

Demnerová Kateřina, prof. Ing. CSc. ( dem...@vscht.cz)
Michova Hana, Ing. Ph.D. ( Han...@vscht.cz)
Despite its fastidious nature, Campylobacter jejuni is continuously reported as the most common cause of foodborne zoonoses. Short genome with simultanously high level of adaptability of C. jejuni suggest that it is capable of rapid change of gene expression resulting in transition from a resilient but metabolically attenuated form outside a host into a virulent and rapidly multiplying form inside a host. This adaptability could be explained by extensive use of quorum sensing systems (QS). The main aims of the thesis involve investigation of the role of QS in lifecycle of C. jejuni, with an emphasis on identification of regulatory pathways mediated by acyl homoserine lactones. Significant part of the thesis will be dedicated to establishing the role of a host-like environment in signalling and pathogenicity of C. jejuni.
Faculty of Food and Biochemical Technology

Relationship between plants endophytes, and its metabolome

Lovecká Petra, doc. Ing. Ph.D. ( lov...@vscht.cz)
Recently, research focused on uncommon natural sources and unexplored habitats has become a subject of deep scientific interest. Exclusive relationships of endophytic bacteria and fungi with plants were shown to have a great potential to produce new and rare secondary metabolites, with unique health beneficial, technological and nutritional properties. The essence of the thesis will be studying of mutual relationships between microbial endophytes and plants by advanced tools of modern analytical chemistry – high resolution mass spectrometry-based metabolomic fingerprinting / profiling. In addition to this, potential ofendophytes to prevent pathogenic fungi growth and mycotoxins production will be assessed.
Faculty of Food and Biochemical Technology

Studying speciation of arsenic in the mycosphere - from microorganisms to animals

Kotrba Pavel, prof. Ing. Ph.D. ( kot...@vscht.cz)
Sácký Jan, Ing. Ph.D. ( SAC...@vscht.cz)
The goal of this work is to answer questions related to not so well studied biotransformations of arsenic in living organisms, with emphasis on fungi. Arsenic is rather toxic, but since it is ubiquitous, organisms have evolved various methods of As detoxification, including redox reactions, methylation and other biotransformation reactions. We suppose, that these bioprocesses are dependent on many factors, including As bioavailability and genetic background of each organism, and various compounds of the so called mycosphere, i.e. all factors related to fungi (geochemistry, microbiome, fungivores). Each factor and process of the biotransformation can thus be studied from a different perspective. The primary goal of this work will be identification, isolation and functional characterization of genes potentially playing role in As transformation in fungi and bacteria and their screening by metagenomic techniques in soil samples and fungal sporocarps. A second approach will deal with growing fungal mycelia in substrate amended with As and assessing the potential of the mycelia to transform inorganic As forms to organic by mass spectrometry. Both these approaches should answer questions such as: Can fungi methylate As? Do As forms correlate with fungal phylogeny? Can fungal As hyperaccumulators change the speciation of As in soil and thus in the surrounding bacterial community? How are As compounds transformed and translocated in the mycosphere?
Faculty of Food and Biochemical Technology

The non-specific phospholipases C from Arabidopsis thaliana: structure-function relationship

Lipovová Petra, doc. Ing. Ph.D. ( kar...@vscht.cz)
Dohnálek Jan, Ing. Ph.D. ( Jan...@ibt.cas.cz)
This PhD work aims to elucidate the catalytic mechanism, structure and structure - function relationship of non-specific phospholipase C (NPC) from Arabidopsis thaliana. Six genes encoding NPCs (NPC1-NPC6) have been identified in the Arabidopsis thaliana genome. In our previous experiments with NPC4, it was found that this enzyme produces, besides the expected product - diacylglycerol, surprisingly also phosphatidic acid. This second activity seems to have been overlooked so far. In this project we will focus on the study of this phenomenon by mutagenesis and try to elucidate the structure and catalytic mechanism of these enzymes. The effect of mutations on plant phenotype will also be investigated.
Updated: 11.12.2019 11:36, Author: Jan Kříž

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