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Graphene oxide (GO) and its ability to detect and capture bacteria and viruses
Roupcová, Petra ; Klouda, Karel ; Kleinová, Sabina
In recent years, advances in nanomaterials research have led to an increase in their various applications in almost every conceivable field, from electrodes to membranes to sports equipment and clothing. Graphene, graphene oxide (GO) and reduced graphene oxide (rGO) are becoming increasingly popular, mainly due to their extraordinary properties and structure. This paper summarizes the potential use of graphene oxide for trapping bacteria and viruses and other potential applications, especially in light of the ongoing coronavirus crisis.
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Morphogenesis of bacterial colonies
Čepl, Jaroslav ; Markoš, Anton (advisor) ; Konopásek, Ivo (referee) ; Nemec, Alexandr (referee)
The topic of this thesis has been built on previous work of our group, especially Rieger et al. 2008 and Čepl et al. 2010. We examined and described the regularity of morphogenesis of S. marcescens, morphotype F colonies (from "the fountain", because of a shape it resembles). Typical colony consists of elevated red navel, low non-pigmented ring and again elevated red rim. Structured profile of the colony together with changes in pigmentation of structures during development without need of artificial dying, provides considerable advantage in observation of the morphogenesis. Aims of this thesis were (i) to find other factors that affect the morphogenesis, (ii) to characterize interactions of S. marcescens colonies with other bacterial strains (S. rubidaea and E .coli) and finally (iii) to study the phenomenon of induced resistance to the antibiotics described in (Heal and Parsons, 2002; Lu 2004; Bernier et al. 2011) in our model organisms. (i) Mutual interactions of colonies on the plate indicates that morphogenesis is affected by autocrine signals, which diffuse into the medium and the atmosphere and affect the development of surrounding colonies. We have detected changes of pH of the medium during the development of colonies in their vicinity. At ...
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BacSeqer: Read simulator for bacterial RNA-Seq
Fialová, Adéla ; Sedlář, Karel
The RNA-Seq method has become a key tool in transcriptomics, providing deep insight into the genetic functioning of organisms. It is essential for understanding how genes are expressed, for discovering new gene variants and for understanding pathologies at the genetic level. RNA-Seq simulators are great for testing and validating bioinformatics tools, they offer a way to compare different computational algorithms and allow examining different sequencing protocols, parameter settings and sample sizes to ensure the most efficient use of resources. This study introduces BacSeqer, an RNA-Seq simulator specifically designed for bacterial transcriptomes with the aim of producing data that faithfully resembles those obtained in real experiments. It allows to take into account the specificities of the bacterial genome, especially an existence of only exons and their organization in operons that are not normally present in eukaryotes.
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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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