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Fleas as hosts and vectors of bacteria
Hovorková, Jana ; Hammerbauerová, Iva (advisor) ; Myslivcová Fučíková, Alena (referee)
Fleas (Siphonaptera) are worldwide significant ectoparasites and vectors of several human pathogens. The most serious flea-born infections include plague, rickettsiosis and bartonellosis caused by Yersinia pestis, Rickettsia spp. and Bartonella spp. I have focused on the microbiome of fleas with an emphasis on bacteria which are transmitted by fleas or are pathogenic, mutualistic or commensal in relation to their flea host, from the point of view of their mutual interactions. The composition of the flea microbiome can be influenced both by mutual interactions between individual bacteria and by many different factors, which include, for example, the species or gender of flea or its host, humidity and temperature of the environment or geographic location.
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Bacterial enzyme activities and molecular mechanism of the decomposition of bone tissue
Vočadlová, Michelle ; Sládek, Vladimír (advisor) ; Mihalčinová, Zuzana (referee)
Abstract The decomposition of bone tissue is a complex process in which bacterial enzymes play a crucial role. Enzymes are biological catalysts involved in all biochemical reactions in living organisms. In this bachelor thesis, bacterial enzymes involved in the breakdown of bone tissue are identified and characterized. The main focus is on various collagenases, which play a key role in the degradation of the organic components of bone. The work also describes the molecular mechanisms by which these enzymes operate. The thesis focuses on specific interactions between bacterial enzymes and the bone matrix, including adhesive interactions and enzyme synthesis responding to specific microenvironments of bone tissue. Factors such as pH, temperature, and the presence of potential inhibitors influence the activity of these bacterial enzymes. These factors contribute to the variability of decomposition processes. Subsequent understanding of the molecular mechanisms by which bacterial enzymes degrade bone tissue has significant applications in forensic science for estimating the time of death, in archaeology for interpreting historical and prehistoric finds, and in medicine, where this research may be important for the diagnosis and treatment of bone diseases. Keywords: Bacterial enzyme, bacteria, bone, collagen,...
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Identification of unknown bacterial genomes using an online database tool
Nejezchlebová, Julie ; Čejková, Darina (referee) ; Schwarzerová, Jana (advisor)
This master's thesis deals with the develop of an automatic software tool - Bacterial Explorer which allows the discovery of unknown bacteria using available bioinformatics tools. The tool is developed in accordance with the requirements of the Veterinary Research Institute (VRI) and is tested on data from the provided VRI database. The theoretical part is dedicated to the description of bacterial typing, methods used for genomic analysis, and already available tools for bacterial typing. In the practical part, the thesis focuses on the implementation of the automatic software tool called Bacterial Explorer, including a description of the tools behind the created tool, the user interface and implementation in the online database of VRI . The final part of the practical section deals with tool testing and discussion of the results.
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Read simulator for bacterial RNA-Seq
Fialová, Adéla ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
This thesis is dedicated to the analysis of the bacterial genome, measurement of its expression mainly by RNA-Seq technology and simulation of RNA-Seq data. The first part of the thesis provides a theoretical background on the structure of the bacterial genome, its expression and methods to study it, including modern sequencing techniques. Several selected simulators of RNA-Seq data are also mentioned. In the second part, the actual simulator implementation is presented, designed to take into account the characteristics of the bacterial genome, in particular the presence of operons.
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Laboratory database for bacterial sample data cataloguing
Podrazký, David ; Bezdíček, Matěj (referee) ; Vítková, Helena (advisor)
Proper handling of the results of typing methods for classification of bacteria is essential for diagnosis and monitoring the spread of infections in the hospital environment. The solution for their management is a relational database. The problem is storing large amounts of multidimensional data due to the variability of typing methods. At the same time, the database needs to be adapted to the requirements of the specific healthcare facility. This thesis describes the design and creation of a relational database for the Centre of Molecular Biology and Genetics at the University Hospital Brno. It discusses the key steps in database development, including data structuring, table and session creation and user interface design.
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Pseudomonas aeruginosa jako původce močových infekcí
ŽÁČEK, Jakub
This bachelor thesis deals with the microbiological laboratory diagnosis of urinary bacterial infections, with an emphasis on the gram-negative bacterium Pseudomonas aeruginosa. This bacterium is known for its high resistance and is often found as a causative agent of urinary infections in immunocompromised patients. The theoretical part of this bachelor thesis describes the structure of the urinary system, bacterial urinary infections as a whole, and the bacterium Pseudomonas aeruginosa itself. The methodological part, conducted in the microbiology section of the SYNLAB České Budějovice laboratory, subsequently describes the procedures for processing urine samples for bacteriological examination, including sampling, transport, and sample reception, pre-cultivation screening, and cultivation methods. Furthermore, methods of identification based on the biochemical properties of bacteria and identification using MALDI-TOF are described. Also included in the methodological part is the determination of bacterial sensitivity to antimicrobial agents using the disc diffusion method. The results obtained from the laboratory information system for the periods of November and December 2023 and January 2024 are evaluated and compared with the results of other authors. This work serves to verify the methods used and emphasizes the use of modern methods in the diagnosis of bacterial urinary infections.
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Molecular detection of Mycoplasma gallisepticum based on whole genome data
KURÁŽ, Jakub
This thesis reviews the basic knowlegde of a bacteria Mycoplasma gallisepticum and attempts to propose a functional detection protocol to distinguish M. gallisepticum from related species of the genus Mycoplasma. Real time PCR optimalization has refined the specificity and increased the efficiency of detection of selected genomic loci for M. gallisepticum. The functionality and accuracy of the method was verified in laboratory experiments by detecting the occurrence of M. gallisepticum in mixed Mycoplasma samples.
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Changes of microbial growth during use of face masks from different materials
Korvasová, Lucie ; Hoová, Julie (referee) ; Márová, Ivana (advisor)
Due to the current spread of Covid-19 disease, there are many types of respiratory protective equipment on the Czech market. However, due to the conditions that breath creates on the inside of the masks, they can be an ideal place for multiplication of microorganisms such as yeasts, moulds and especially bacteria. Since various protection masks differ in their production materials, bacteria colonization won’t always be the same. The subject of the thesis is a comparison of individual types of masks and respirators with regard to multiplication of microorganisms in their structure, which were tested using the contact stamp-form method on agar plates and in a liquid medium. Sterile environment was required during the work to avoid external contamination. Methods of imprinting on agar plates and the fact that turbidity and thus measurable absorbance increases with rising number of microorganisms were used to obtain the data. Result of the work was that face masks already contained some level of contamination from their production. As the best kind of face masks in terms of multiplication of microorganisms came out cotton, which prevented multiplying in the inoculated sphere. At the same time each growing culture was tested for viability, where it was determined how many viable cells each sample contained in comparison to a fully grown culture.
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Functional annotation of non-model bacteria based on sequential homology
Polakovičová, Petra ; Musilová, Jana (referee) ; Sedlář, Karel (advisor)
Genomová sekvence je důležitým zdrojem informací v oblasti biologie, a proto je neustálým předmětem zájmu vědeckého výzkumu. Na práci s genomem a jeho analýzu nabízí bioinformatika různé výpočetní metody. Tato práce se věnuje bakteriálnímu genomu, jeho organizaci, základním vlastnostem a následně popisuje jeho anotaci. Zaměřuje se hlavně na funkční anotaci (popis biologické funkce predikovaných genů) na základě přiřazení takzvaných klastrů ortologních genů (COG) s využitím sekvenční homologie. Popisuje nejpoužívanější nástroje a databáze, které se využívají pro COG anotaci a poté několik z nich porovnává při anotaci sedmi bakteriálních genomů. Jejím hlavním cílem je navrhnout metodu, která vylepší COG anotaci a zjednoduší její výslednou vizualizaci.
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Study of the chemical processes during kombucha technology
Chludilová, Markéta ; Obruča, Stanislav (referee) ; Pořízka, Jaromír (advisor)
The kombucha drink is referred to as leavened tea with added sponge called a scobie. In this way, a low-alcohol beverage is obtained, which gains considerable popularity, especially due to the alleged beneficial properties for human health. The microbial composition of this beverage is very rich, consisting of bacteria and yeasts living in a beneficial symbiosis [11]. The microbial composition of the drink and its beneficial effects on human health are very closely related. This work deals with the analysis of the chemical composition of the commodity beverage, especially with regard to the content of major components such as organic acids, carbohydrates and ethanol. These analytes are among the most common and most profoundly found substances in the carbohydrate beverage and are very closely related to the microbial composition of the scoby itself [3]. Combo beverage samples were supplied by RebornFood, one of which is the commercial production of this drink on the Czech market. At the same time, this company bases itself on purely natural fermentation of beverages, and therefore it is not particularly involved in the production process. The results of this diploma work point to the effect of the scoby used and the associated occurrence of analytes in the beverage, as well as the production process associated with the formation of analytes, which is described in several articles. It is expected that this work will provide information both on the production conditions and on the chemical properties of the beverage related to the condition of the scoby, which will be used further, both for RebornFood and the material used to solve the technical problems of this beverage production.
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