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Analysis of single-cell genomic data of Saccinobaculus sp.
Gajdošová, Petra ; Treitli, Sebastian Cristian (advisor) ; Kolísko, Martin (referee)
The progress of single-cell genomics and metagenomics techniques allows us to explore the uncultured organisms in greater depth. In this work, we focused on the genome assembly and genetic code of the oxymonad Sacinobaculus ambloaxostylus, which inhabits the hindgut of wood-eating cockroaches from the genus Cryptocercus. Using single cell picking and whole genome amplification we obtained sequencing data from three cells of S. ambloaxostylus. The obtained data was used to generate a single-cell genome assembly using SPAdes. The assembly was further binned and decontaminated to remove any potential bacterial or eukaryotic contaminants. After decontamination and re-assembly, we obtained a genome assembly with a total length of ∼417Mbp distributed to ∼185 thousand scaffolds. Despite its low completeness of 13.71%, we attempted to determine the genetic code used by S. ambloaxostylus. For this we manually modeled 33 genes from various metabolic pathways. Aligning these gene models with homologs from closely related oxymonads, we calculated the usage of stop codons as sense codons with focus on conserved positions. Our results suggest that the stop codons UAA and UAG act as sense codons and most probably they encode glutamine. Our 18S rRNA phylogeny was unable to answer the question if the ciliate...
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Structural identification of protein-DNA interactions using machine learning
Gajdošová, Petra ; Hoksza, David (advisor) ; Feidakis, Christos (referee)
DNA-protein interactions are essential parts of cell life and cell cycle. Prediction of these interactions requires knowledge of DNA and a protein structure. Because machine learning approaches show adequate results in biological predictions, we chose to use it for the prediction of protein-DNA interactions. In this thesis, we use the machine learning tool P2Rank that was originally designed for prediction of ligand-binding sites and adapt it to predict DNA-binding sites. Apart of that, the thesis serves as a summary of existing prediction tools/methods and includes suggestions for further modifications of P2Rank.
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Analysis of the use of potentially inappropriate cardiovascular drugs in seniors in acute care in the project EUROAGEISM H2020
Gajdošová, Petra ; Fialová, Daniela (advisor) ; Pokladníková, Jitka (referee)
Title: Analysis of the use of potentially inappropriate cardiovascular drugs in seniors in acute care in the project EUROAGEISM H2020 Author: Petra Gajdošová Department: Department of Social and Clinical Pharmacy Supervisor: Assoc. Prof. PharmDr. Daniela Fialová PhD. ABSTRACT INTRODUCTION: Population aging is a global problem for which all health and social systems of all countries needs be prepared, including the Czech Republic. It is assumed that in 2050 every third citizen of the Czech Republic will be 65 years and older. The group of seniors is characterized by high polymorbidity and polypharmacotherapy. Prescription of drugs is also very complicated in seniors due to changes accompanying aging (at the level of pharmacokinetics, pharmacodynamics and homeostasis). The aim of this diploma thesis was to determinate the prevalence of potentially inappropriate medications (PIMs) from the cardiovascular system (CVS) using the best-known explicit criteria of PIMs in the Czech sample of seniors in acute care assessed during the FIP7 program of the EUROAGEISM H2020 project. METHODOLOGY: Data collection was held during the FIP7 program of the EUROAGEISM H2020 project in acute care in seniors aged 65 years and over in two health facilities in Brno and Hradec Králové (HK) in the Czech Republic from August 2018 to...
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Aromatické sloučeniny obsažené v mátě zjištěné metodou plynové chromatografie
Gajdošová, Petra
For species Mentha x piperita, Mentha spicata and Mentha longifolia grown on land Mendel University in Lednice, was evaluated morphological structure and content of aromatics in the species Mentha x piperita and Mentha spicata. They were found large differences between species in the evaluation of morphological characteristics and they were found differences within species too. It was confirmed that the genus Mentha is a very variable species. The content and composition of the aromatics in the extrudate from the plant Mentha x piperita and Mentha spicata were researched by the method SPEM-GC/MS. The main components of the species Mentha x piperita were: (-) - menthol, linalool, (Z) -a-farnesene, eugenol, alpha-pinene, (z) -citral, limonene, linalool, (E) -2-hexanal, 3-octanone , 3-methyl-1-butanol, methyl acetate. The type of Mentha spicata had the highest content of substances: (-) - menthol, linalool, (Z) -a-farnesene, (z) -citral, alpha pinene, eugenol, alpha-citronellol, (E) -2-hexanal, 3 -octanone, 3-methyl-1-butanol, methyl acetate. The most important and most dominant aromatic compound was menthol.
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