|
Programme Details
| Study Language
|
Czech |
|
Standard study length
|
4 years |
| Form of study
|
combined
,
full-time
|
| Guarantor
|
prof. Ing. Bc. Ondřej Uhlík, Ph.D.
|
| Place of study
|
Praha |
| Capacity
|
10 students |
| Programme code (national)
|
P0511D130021 |
| Programme Code (internal)
|
D301
|
| Number of Ph.D. topics
|
8 |
Ph.D. topics for study year 2025/26
Diagnosis of infectious diseases of the central nervous system
|
Study place:
|
Institute of Microbiology of the CAS
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
Institute of Microbiology of the CAS
|
|
Also available in study programmes:
|
Microbiology (
in English language
)
|
| Supervisor: |
prof. Ing. Vladimir Havlíček, Dr.
|
| Expected Form of Study: |
Full-time |
| Expected Method of Funding: |
Salary |
Annotation
Central nervous system infections cause acute changes in mental and physical brain functions, leading to chronic impairment of cognitive, memory, and motor abilities. These changes are related to alterations in brain neuronal signaling in susceptible brain regions. This Ph.D. topic aims to utilize matrix-assisted laser desorption/ionization-mass spectrometry imaging and highly multiplex immunohistochemistry-based mass spectrometry imaging to analyze and quantify molecular interactions between host and pathogen in cases of neuroaspergillosis caused by Aspergillus fumigatus and pneumococcal meningitis caused by Streptococcus pneumoniae. The Ph.D. project will determine the optimal transport mechanism for microbial secondary metabolites, such as toxins and quorum sensing molecules, across the blood-brain barrier. The study will analyze the impact of microbial metabolites on neurotransmitter signaling, specifically through the dopaminergic and glutamatergic pathways, in critically affected brain regions. The candidate biomarkers will successfully diagnose CNS infections in human cerebrospinal fluid samples based on the host-pathogen molecular fingerprint.
Phylogenetically novel and metabolically rare prokaryotes of geothermally heated groundwaters
|
Study place:
|
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
|
| Supervisor: |
prof. Ing. Bc. Ondřej Uhlík, Ph.D.
|
| Expected Form of Study: |
Full-time |
| Expected Method of Funding: |
Scholarship + salary |
Annotation
Geothermally heated groundwater has attracted the attention of microbiologists for decades due to its unique chemical and thermal profiles. Analyses of these unique ecosystems have identified many novel clades in the tree of life, both bacterial and archaeal in origin. Although western Bohemia hosts many curative thermal springs that are considered national treasures, their microbial life remains virtually unstudied. Our preliminary analyses have revealed the tremendous microbial diversity of these unique ecosystems, far exceeding expectations in terms of both phylogenetic and functional/metabolic novelty. The aims of this doctoral dissertation will be to explore novel prokaryotic lineages from various thermal water samples and analyze their metabolic potential, phylogeny, and ecology. The work will be executed within the framework of the Czech Science Foundation grant project 25-15226S entitled Hidden Gems of Microbial Diversity: Geothermally Heated Groundwaters as a Source of Phylogenetically Novel and Metabolically Rare Prokaryotes.
Secondary metabolism of intracellular pathogens
|
Study place:
|
Institute of Microbiology of the CAS
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
Institute of Microbiology of the CAS
|
|
Also available in study programmes:
|
Microbiology (
in English language
)
|
| Supervisor: |
prof. Ing. Vladimir Havlíček, Dr.
|
| Expected Form of Study: |
Full-time |
| Expected Method of Funding: |
Salary |
Annotation
The PhD candidate will study, correlate and mine the metabolism of intracellular pathogens within host cells. The candidate can solve five pressing diagnostic problems of our time, and together with the Stanford University, can address the dynamic range of analytical chemistry in mapping and quantifying intracellular pathogens in the host. Through this collaboration, the applicant will be able to work with isogenic strains, i.e., will always have host systems with very similar metabolomics and identical host genetic makeup. All directions of intracellular research are of the highest societal importance and involve the endemic fungus Coccidioides immitis, a Pf4 bacteriophage in the Gram-negative bacterium Pseudomonas aeruginosa, the AfPmV-1 polyomavirus in the filamentous fungus Aspergillus fumigatus, and the betaproteobacterium Mycetohabitans endofungorum, an intracellular symbiont of the filamentous fungus Rhizopus microsporus. Also a contribution to a novel diagnostic for Mycobacterium tubercullosis in mammalian cells is expected. The applicant will use the portfolio of infection metallomics, a set of dependent mass spectrometry, separation, and computational techniques.
Micropollutants and their impact on the environment
|
Study place:
|
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
|
| Supervisor: |
doc. Ing. Hana Stiborová, Ph.D.
|
| Expected Form of Study: |
Full-time |
| Expected Method of Funding: |
Scholarship + salary |
Annotation
The environment is continuously exposed to the harmful effects of foreign substances with toxic properties. These substances are produced and used across various industries, including the pharmaceutical industry, with the consumption of pharmaceuticals in human medicine steadily increasing. Although these substances often occur at very low concentrations, repeated exposure can lead to negative environmental impacts. This thesis will evaluate the effect of different mixtures of micropollutants, such as pharmaceuticals, antimicrobials, and plasticizers, on the soil-plant system. The thesis will investigate how micropollutants affect microbial communities in the soil, rhizosphere, and endophytic microorganisms, while assessing the accumulation and transport of micropollutants by plants. Special attention will be given to the interaction between micropollutants and arbuscular.
The role of capsid protein structure and function in the life cycle of retroviruses
|
Study place:
|
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
|
| Supervisor: |
doc. Ing. Jan Lipov, Ph.D.
|
| Expected Form of Study: |
Combined |
| Expected Method of Funding: |
Not funded |
Annotation
Rational control of retroviruses requires a detailed understanding of the basic mechanisms that influence key steps in their life cycle. This research will focus on the analysis of structural elements of the capsid protein, which are essential for the formation and stability of the retroviral particle and for interaction with other viral proteins. First, various forms of structural proteins will be recombinantly prepared in sufficient quantity and purity, which will subsequently be used to produce virus-like particles. Furthermore, the effect of mutations of selected amino acids and the action of small charged molecules on the formation and stability of these particles will be investigated. The results of this research may contribute significantly to the development of new antiviral strategies and drugs.
Role of Specific Bacteria and Their Metabolic Pathways in Degrading Lignin and its Structural Motifs
|
Study place:
|
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
|
| Supervisor: |
prof. Ing. Bc. Ondřej Uhlík, Ph.D.
|
| Expected Form of Study: |
Full-time |
| Expected Method of Funding: |
Scholarship + salary |
Annotation
Lignin is the second most abundant biopolymer on Earth after cellulose and contains approximately 30% of the carbon in the biosphere. This complex plant biopolymer, consisting of phenylpropanoid units, is of considerable ecological and industrial importance. Although the synthesis of lignin in plants is well understood, its degradation by soil microorganisms is still not fully understood. Fungi, especially basidiomycetes (white rot fungi) and ascomycetes, are considered to be the main lignin degraders, using enzymes such as laccases and heme peroxidases to depolymerize lignin. However, recent studies suggest that some bacteria, particularly streptomycetes and proteobacteria, also produce enzymes capable of degrading lignin, although our knowledge of bacterial lignin degradation remains fragmentary and incomplete. Soil lignin degradation is also a rich source of phenolic compounds. Many of these substances are structurally similar to anthropogenic pollutants, allowing bacteria to use the same enzymes for their degradation. This process, known as cometabolism, is still not fully understood. Thus, information on the degradation of lignin structural motifs and their role in pollutant cometabolism remains incomplete. The aim of this doctoral dissertation will be to further elucidate the role of bacterial populations in the degradation of lignin and its structural motifs (phenolic compounds) and to better understand the link between this degradation and the degradation of organic pollutants. This will be achieved using (meta)genomic, transcriptomic and metabolomic techniques. The work will be executed within the framework of the Ministry of Education, Youth and Sports of the Czech Republic OP JAK grant Talking Microbes - understanding microbial interactions within One Health framework (CZ.02.01.01/00/22_008/0004597).
Impact and Mechanism of Action of Nanodiamond Materials on Selected Microorganisms
|
Study place:
|
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
|
| Supervisor: |
doc. Ing. Hana Stiborová, Ph.D.
|
| Expected Form of Study: |
Full-time |
| Expected Method of Funding: |
Scholarship + salary |
Annotation
Understanding the interactions between nanodiamond (ND) materials and microorganisms is crucial for both fundamental and applied research. This includes the development of functional biosensors, materials based on nanodiamond thin films with antimicrobial effects, and rapid detection of microorganisms. Nanodiamonds can have a widely tunable surface charge, be stabilized by bonding into nanocomposites, and be decorated with metallic nanoparticles. These mechanisms can affect not only their electro-optical properties but also their interactions with microorganisms. Within the mechanism of ND action on microorganisms, factors such as affinity to the cell surface, penetration through the cell wall, the influence of ND size, their zeta potential, shape, sp2/sp3 structure, and surface chemical composition will be evaluated. The dissertation will also focus on their subsequent applications, for example, as part of sensors.
Effect of morphology and surface topography of nanomaterials on interactions with microbial cells
|
Study place:
|
Department of Biochemistry and Microbiology, FFBT, VŠCHT Praha
|
| Guaranteeing Departments: |
Department of Biochemistry and Microbiology
|
| Supervisor: |
prof. Ing. Kateřina Demnerová, CSc.
|
| Expected Form of Study: |
Full-time |
| Expected Method of Funding: |
Scholarship + salary |
Annotation
Nanofibrous materials have a wide range of applications in medicine, the food industry and biotechnology, where their microbiological safety is essential. Current research shows that the interaction of nanofibers with microbial cells can be influenced by modifying the morphology and topography of the nanofibers. This work will focus on studying the influence of key factors, mainly fibre diameter, areal weight and sharp micro/nano-structures on the nanofiber surface, on interactions with microbes relevant to the aforementioned areas. The aim will be both to reduce the adhesion of pathogens to medically and food-applicable materials and to maximise the biofilm formation of probiotic microorganisms when using nanomaterials as their carriers for large-scale production. The study will use both culture and modern microbiological, microscopic and molecular biological methods.
|
