Methods for gene prediction in prokaryotic genomes

Tato bakalářská práce se zabývá metodami predikce genů v prokaryotických organismech. V první části je popsána prokaryotická buňka včetně genomu, exprese genetické informace a rozdělení metod pro predikci genů. Dále je zde uveden popis tří vybraných softwarů, které predikci provádějí. V praktické části je rozebráno testování softwarů a vyhodnocení jejich účinnosti na daném genomu. Nakonec je zde popsán vytvořený program pro hledání genů a jsou zde uvedeny výsledky jeho účinnosti.This bachelor thesis deals with methods of gene prediction in prokaryotic genomes. First part of the thesis introduces prokaryotic cell, its genome, expression of genetic information and methods for gene prediction. Following part describes three software products for gene prediction. Chosen software was tested against specific genome and next chapter presents obtained results. The last part describes program called Gene_finder and its results.

Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov., two multidrug-resistant psychrotrophic species isolated from Antarctica

Despite unfavourable Antarctic conditions, such as cold temperatures, freeze-thaw cycles, high ultraviolet radiation, dryness and lack of nutrients, microorganisms were able to adapt and surprisingly thrive in this environment. In this study, eight cold-adapted Flavobacterium strains isolated from a remote Antarctic island, James Ross Island, were studied using polyphasic taxonomic approach to determine their taxonomic position. Phylogenomic analyses based on 16S rRNA gene and 92 core genes clearly showed that these strains formed two distinct phylogenetic clusters comprising three and five strains, with average nucleotide identities significantly below 90 % in between both proposed species as well as between their closest phylogenetic relatives. Phenotyping revealed a unique pattern of biochemical and physiological characteristics enabling differentiation from the closest phylogenetically related Flavobacterium spp. Chemotaxonomic analyses showed that type strains P4023T and P7388T were characterized by the major polyamine sym-homospermidine and a quinone system containing predominantly menaquinone MK-6. In the polar lipid profile phosphatidylethanolamine, an ornithine lipid and two unidentified lipids lacking a functional group were detected as major lipids. These characteristics along with fatty acid profiles confirmed, that these species belong to the genus Flavobacterium. Thorough genomic analysis revealed presence of numerous cold-inducible or cold-adaptation associated genes, such as cold-shock proteins, proteorhodopsin, carotenoid biosynthetic genes or oxidative-stress response genes. Genomes of type strains surprisingly harboured multiple prophages, with many of them predicted to be active. Genome-mining identified biosynthetic clusters in type strain genomes with majority not matching any known biosynthetic genes which indicates further research possibilities involving these psychrotrophic bacteria. Antibiotic susceptibility testing revealed multidrug-resistant phenotype that was correlated with in silico antibiotic resistance prediction. Interestingly, while typical resistance finder tools failed to detect genes responsible for antibiotic resistance, genomic prediction confirmed multidrug-resistant profile and suggested even broader resistance than tested. Results of this study confirmed and thoroughly characterized two novel psychrotrophic Flavobacterium species, for which names Flavobacterium flabelliforme sp. nov. and Flavobacterium geliluteum sp. nov. are proposed

The Professional Speech and Slang of Musicians

The analysis of musicians{\crq} professional speech is the subject of this thesis. The main stress is put to the profiling of various ways the professional speech vocabulary is being enriched: by taking over expressions from foreign languages, semantic forming of lexical units (metaphor, metonymy) and creation of new words. Therefore, the attention is also focused on the word-building structure of the lexical units. Also, the presence or absence of the expressive token is being observed. The goal of the work is to draw attention to the vocabulary of musicians{\crq} professional speech from the linguistical point of view. The explanatory directory of terms used by musicians during excercise of their profession is the integral part of the work. For easier orientation, the index is also included

Genotyping of Klebsiella pneumoniae isolates

Tato diplomová práce se zabývá typizací kmenů bakterie Klebsiella pneumoniae. V první části jsou představeny metody typizace včetně jejich výhod a nevýhod. Následně je charakterizován bakteriální genom a popsána bakterie Klebsiella pneumoniae. V praktické části je uveden postup složení jednotlivých genomů včetně otestování jejich kvality a je představen navržený algoritmus pro nalezení variabilních úseků genů, které vykazují vyšší míru variability. Poté jsou uvedeny získané výsledky, které jsou následně otestovány na dalších genomech Klebsiella pneumoniae.This master thesis deals with typing of Klebsiella pneumoniae isolates. The first part of the thesis introduces molecular typing methods. Then bacterial genomes and Klebsiella pneumoniae are characterized. Following part describes data validation, assembly of genomes and proposed algorithm for finding genes with high variability. In last part obtained results are presented and validated on other genomes of Klebsiella pneumoniae.

Genotyping Of Klebsiella Pneumoniae Isolates

Typing methods capable of distinguishing bacterial strain are essential for epidemiologist because they help to prevent and control infections. Unfortunately, many typing methods are timeconsuming, expensive and reproducibility of their results is questionable. Therefore, we propose a new genotyping method, which is capable of identifying genes with high rate of variability to distinguish different bacterial strains

Diversity and Evolution of Clostridium beijerinckii and Complete Genome of the Type Strain DSM 791T

Clostridium beijerinckii is a relatively widely studied, yet non-model, bacterium. While 246 genome assemblies of its various strains are available currently, the diversity of the whole species has not been studied, and it has only been analyzed in part for a missing genome of the type strain. Here, we sequenced and assembled the complete genome of the type strain Clostridium beijerinckii DSM 791T, composed of a circular chromosome and a circular megaplasmid, and used it for a comparison with other genomes to evaluate diversity and capture the evolution of the whole species. We found that strains WB53 and HUN142 were misidentified and did not belong to the Clostridium beijerinckii species. Additionally, we filtered possibly misassembled genomes, and we used the remaining 237 high-quality genomes to define the pangenome of the whole species. By its functional annotation, we showed that the core genome contains genes responsible for basic metabolism, while the accessory genome has genes affecting final phenotype that may vary among different strains. We used the core genome to reconstruct the phylogeny of the species and showed its great diversity, which complicates the identification of particular strains, yet hides possibilities to reveal hitherto unreported phenotypic features and processes utilizable in biotechnology

Application of mini-MLST and whole genome sequencing in low diversity hospital extended-spectrum beta-lactamase producing Klebsiella pneumoniae population

Studying bacterial population diversity is important to understand healthcare associated infections’ epidemiology and has a significant impact on dealing with multidrug resistant bacterial outbreaks. We characterised the extended-spectrum beta-lactamase producing K. pneumoniae (ESBLp KPN) population in our hospital using mini-MLST. Then we used whole genome sequencing (WGS) to compare selected isolates belonging to the most prevalent melting types (MelTs) and the colonization/infection pair isolates collected from one patient to study the ESBLp KPN population’s genetic diversity. A total of 922 ESBLp KPN isolates collected between 7/2016 and 5/2018 were divided into 38 MelTs using mini-MLST with only 6 MelTs forming 82.8% of all isolates. For WGS, 14 isolates from the most prominent MelTs collected in the monitored period and 10 isolates belonging to the same MelTs collected in our hospital in 2014 were randomly selected. Resistome, virulome and ST were MelT specific and stable over time. A maximum of 23 SNV per core genome and 58 SNV per core and accessory genome were found. To determine the SNV relatedness cut-off values, 22 isolates representing colonization/infection pair samples obtained from 11 different patients were analysed by WGS with a maximum of 22 SNV in the core genome and 40 SNV in the core and accessory genome within pairs. The mini-MLST showed its potential for real-time epidemiology in clinical practice. However, for outbreak evaluation in a low diversity bacterial population, mini-MLST should be combined with more sensitive methods like WGS. Our findings showed there were only minimal differences within the core and accessory genome in the low diversity hospital population and gene based SNV analysis does not have enough discriminatory power to differentiate isolate relatedness. Thus, intergenic regions and mobile elements should be incorporated into the analysis scheme to increase discriminatory power