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Analysis of horizontal transfer of genetic components using static network analysis
Labanava, Anastasiya ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor's thesis focuses on the issue of horizontal genetic elements transfer between bacteria of different strains and the software analysis implementation that enables horizontally transferred genes identification. The packages and tools used were tested on a dataset of bacterial genomes from several strains. The thesis’ theoretical part provides a detailed description of the genetic components transfer between bacteria and describes modern laboratory techniques that enable genome sequencing in various ways. In the practical part, the thesis deals with the preprocessing of genomic files to obtain suitable data for annotation. To detect the horizontal transfer of genetic elements between bacteria, a script is introduced, which organizes annotated bacteria to tables and searches for the same genes in their genomes that, under theoretical assumptions, were horizontally transferred. Furthermore, the gene transfer is visualized using tools that graphically represent phylogenetic relations between bacteria. In the final step, bacterial genomes are connected into networks, and based on their static analysis, a discussion is conducted on the results accuracy and the success of the proposed analysis.
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Metagenomic analysis of animal gut microbioma based on diet
Spanakis, Martin Nikolaos ; Čejková, Darina (referee) ; Bartoň, Vojtěch (advisor)
This bachelor’s thesis deals with the sequencing of the microbiome and its composi- tion. It focuses on the gut microbiome of animals, which differs among animals with different diets. The work describes theoretical knowledge about metagenomic analysis of the microbiome, such as sampling procedures, various sequencing methods and data processing. The practical part of the work includes the preparation of the dataset, which includes the collection of data and their preparation for the following metagenomic anal- ysis. The result of the work is the taxonomic classification of bacterial species in the samples and the analysis of their diversity according to the type of diet of individual animals.
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Influence of second and third generation sequencers on cgMLST analysis of closely-related bacterial strains.
Slavíček, David ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This bachelor thesis is about influence of sequncers of second and third generationon cgMLST analysis of bacterial genome. In the theoretical section were described selected sequencers of second and third generation and genome assembly principles. In the practical part were assembled six genomes of Klebsiella pneumoniae bacteria from University Hospital Brno. The genomes were sequenced each on two different sequencers, Illumina Miseq and Oxford Nanopore Technologies Minion. The genomes were assembled. Suitable genes were selected and insufficient quality genomes removed for the cgMLST analysis. The cgMLST analysis was performed and the results are shownin graphs.
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Comparative and phylogenetic analysis of viruses in the University Hospital Brno
Švestková, Tereza ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This thesis is focused on the SARs-CoV-2 coronavirus associated with severe acute respiratory syndrome, which was first identified in 2019. This coronavirus caused a pandemic that affected almost the entire world. Knowledge of the genetic information is needed for vaccine development, to determine infectivity and to predict the evolution of SARs-CoV-2 variants. To obtain genetic information, RNA must be sequenced and these genomic sequences must be assembled. By comparing the assembled genomes, it is possible to find out which part of the organism has mutated. Phylogenetic analysis is performed on the basis of the concordance or divergence in the assembled genomes, which indicates the evolution of the organism and shows the evolutionary relationship with other organisms. The practical part is focused on the assembly of genomes from samples from patients in the University Hospital Brno and evaluation of the quality of the assembly. After the genomes are assembled, the next goal is to evaluate the variability and subsequent phylogenetic analysis.
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Identification of non-coding RNAs of Clostridium beijerinckii NRRL B-598 using RNA-Seq data
Pomykalová, Barbora ; Sedlář, Karel (referee) ; Jurečková, Kateřina (advisor)
This bachelor thesis contains short introduction into bacterial small non-coding RNA problematic. It is oriented on their features and functions in organisms, especially in bacteria Clostridium beijerinckii NRRL B-598. Bachelor thesis also contains description of various laboratory methods for gene expression determination and suggests a detection method for small non-coding RNA in bacteria Clostridium beijerinckii NRRL B-598. Suggested method works with data, which were obtained by RNA-Seq technology. Within the framework of the bachelor thesis was suggested method implemented in programming and numeric computing platform MATLAB and its results were discussed.
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Properties of current signals in nanopore sequencing
Plocková, Veronika ; Nykrýnová, Markéta (referee) ; Sedlář, Karel (advisor)
Oxford Nanopore technologies brought new and revolutionary technology in the field of DNA sequencing. Their sequencing device measures changes in the electric current flowing through pores together with DNA. This work aims to describe differences between raw signals produced by various sequencing kits and sequencing flowcells while sequencing several different bacteria. Two datasets combining five different organisms, two sequencing kits, and two types of flowcells were used to analyze various statistical parameters that would be suitable for the description of current signals gathered from nanopores. Finally, the samples were classified using the k-means algorithm and the results were discussed.
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Bioinformatic analysis of single nucleotide polymorphisms in the 1000 Genomes Project database
Parobková, Viktória ; Roy, Sudeep (referee) ; Provazník, Ivo (advisor)
Sekvenovanie celého ľudského genómu a nájdenie jeho variácii bolo výzvou počas mnohých rokov. Znalosť všetkých genetických variácií je pozoruhodne prospešná pri výskume chorôb. Táto práca je zameraná na genetické variácie človeka a ich dva hlavné výskumné projekty, The HapMap Project a The 1000 Genomes Project, ktoré pomohli v analýze chorôb. Prvá časť práce je venovaná teoretickému popisu projektov. V nasledujúcej časti práce sú popísané štruktúry databáz u oboch projektov a taktiež je predstavený online nástroj umožňujúci prehľadávanie a sťahovanie ich dát. Následne je prevedená štatistická, populačná a bioinformatická analýza štrukturálnych variácií produkovaných 3 fázou 1000 Genomes projektu.
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Taxonomic classification of yeasts associated with meadow plants
Čurillová, Natália ; Ing.Hana Dudášová, Ph.D. (referee) ; Horváthová, Ágnes (advisor)
In total 60 yeast strains isolated from meadow flowers were selected for identification using MALDI-TOF biotyping. Selected yeast strains were prepared according to standard (Bruker) method and method developed at Institute of Chemistry SAS in Bratislava for MALDI-TOF yeast identification. To acquire valuable data two cultivating media were used. The principle of identification embody in comparing obtained mass spectra according to the score of selected yeast strain isolated from meadow plants, formerly identified by physicobiochemical properties (verification of their taxonomic classification) or the new isolates (their identification) with mass spectra of the reference yeast cultures. Reference yeast cultures were identified by sequencing the D1/D2 of 26S rRNA domain. In total 53 yeast strains were identified by biotyping at species level. The remaining 7 yeast strains were designed to be identified by sequencing the D1/D2 26S rRNA domain as the reference mass spectra were not available. The highest abundance of yeast species was as follows Metschnikowia pulcherrima (12 %), Rhodotorula spp. (12 %), Cystofilobasidium infirmominiatum (10 %), Metschnikowia reukaufii (7 %), Metschnikowia fructicola (7 %), Sporobolomyces metaroseus (7 %), Hanseniospora uvarum (5 %), Rhodotorula mucilaginosa (5 %), Meyerozyma guillermondii (5 %), Cystofilobasidium macerans (3 %) a Rhodotorula dairenensis (3 %), and yeast strains of species Candida bombi, Pichia kudravzievii, Cystofilobasidium capitatum, Cystofilobasidium macerans, Solicoccozyma aeria, Sporidiobolus salmonicolor, Papiliotrema flavescens, Sporidiobolus metaroseus, Sporidiobolus pararoseus and Cryptococcus wieringae were identified as well. In general, the most diverse abundance of yeast species were isolated from meadow plants comparing to the older studies.
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