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Microbiology

Microbiology

CHYBI CHARAKTERISTIKA PROGRAMU

The purpose of the study programme is to train specialists with a comprehensive understanding of microbial populations, their activity, phylogenetic and metabolic diversity, mechanisms controlling targeted changes of their genetic information or chemical principles affecting the relationship within microbial communities. The study programme is based on the combination of various forms of tuition and laboratory research, with the main emphasis on independence, initiative and critical approach of students. Alumni of this study programme should be able to routinely use any of the acquired knowledge, skills and competences for industrial or other applications.

Careers

Alumni of this study programme should have a comprehensive microbiological, biochemical and engineering background that will enable them to fully understand the microbial world. They will dispose of deep theoretical insight as well as practical skills in all key areas of microbiology, including biochemistry of microorganisms, molecular biology, genetic engineering and other closely related fields. The alumni of the study programme will find employment in all areas of biotechnology, food, pharmaceutical or chemical industry, in clinical laboratories, in the field of environmental sciences and agriculture. Last but not least, the alumni should be highly competent to work in academia.

Programme Details

Language of instruction English
Standard length of study 4 years
Form of study Full time + Combined
Guarantor of study programme None
Programme Code AD301
Place of study Prague
Capacity 15 students
Number of available PhD theses 4

List of available PhD theses

Heterogeneity of expression of effectors of Salmonella pathogenicity island 2?encoded type 3 secretion system

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Mikrobiologie
Theses supervisor: RNDr. Ondřej Černý, Ph.D.

Response of microbial communities to changing climate in Arctic tundra soils

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Mikrobiologie
Theses supervisor: RNDr. Jana Voříšková, PhD.

Annotation

Climate models predict substantial changes in temperature and precipitation patterns across the Arctic regions in future decades. Microbes are known to play key roles in determining the stability of soil carbon and its possible release into the atmosphere as greenhouse gases. Carbon-rich Arctic soil ecosystems are particularly vulnerable to carbon losses due to warming and subsequent ecosystem disturbances as wildfires. The aim of the project will be to explore the response of soil microbial communities to the conditions caused by future climate change, specifically increased winter precipitation, summer warming and wildfire disturbance. For the project, we will use the experimental sites in western and southern Greenland, maintained by University of Copenhagen, which simulate predicted changes in soil ecosystem. Microbial communities from collected soil samples will be characterized using state-of-the-art methods of molecular biology.

Structure-Function Relationships of the Bordetella Type III Secretion System Proteins

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Mikrobiologie
Theses supervisor: prof. Ing. Peter Šebo, CSc.

Annotation

Type III secretion systems are membrane-embedded nanomachines used by many Gram-negative pathogens to inject bacterial effector proteins into the cytosol of eukaryotic cells. The aim of this thesis is to depict structure-function relationships of proteins of Bordetella III injectosome and its secreted substrates. Specifically, BopN protein that exhibits homology to the class of “gatekeepers” or “plug” proteins, Bsp22 protein that forms a unique filamentous T3SS tip complex and BteA effector protein with unknown mechanism of action. The PhD. candidate will develop reporter assays to analyze activity of Bordetella type III secretion system, perform super-resolution and cryo-electron microscopy and further carry out structural characterization and crystallization trials of the purified recombinant proteins, their domains and/or their mutated variants.

Virulence Mechanisms of the genus Bordetella

Department: Department of Biochemistry and Microbiology, Faculty of Food and Biochemical Technology
Also available in programme: Mikrobiologie
Theses supervisor: RNDr. Jana Kamanová, Ph.D.

Annotation

Pathogenic Bordetella species cause respiratory infections in mammals. While B. bronchiseptica is primarily an animal pathogen, B. pertussis is the causative agent of the whooping cough disease in humans. The PhD thesis aims to reveal the novel mechanisms of Bordetella virulence by genome-wide CRISPR/Cas9-mediated screen. A pool of knock-out human epithelial cells will be generated by an already validated gRNA library. Following Bordetella infection, the candidate genes that confirm the sensitivity of epithelial cells to Bordetella cytotoxicity will be determined. The hits will be further validated and their role in susceptibility to Bordetella infection confirmed.


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