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Typing of bacterial populations based on methylation site detection
Hlavatá, Kristína ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Táto bakalárska práca sa zameriava na detekciu metylácií DNA a vývoj metodiky typizácie bakteriálnych kmeňov. DNA metylácie hrajú kľúčovú úlohu ako regulačný mechanizmus v genóme, ktorý ovplyvňuje konečné vlastnosti organizmov. Použili sme DeepSignal2 na detekciu metylačných vzorov v 10 kmeňoch Klebsielly pneumoniae. Okrem toho sme navrhli metódu typizácie na základe identifikovaných metylácií pre kategorizáciu bakteriálnych kmeňov. Táto práca prispieva k zlepšeniu našeho chápania regulačných mechanizmov v bakteriálnych genómoch a predstavuje nový prístup k typizácii kmeňov pomocou vzorov metylácie DNA. Poskytuje cenné poznatky o charakterizácii a klasifikácii bakteriálnych kmeňov na základe ich metylómov.
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Molluscs as a new model system in molecular biology
Ber, Tobiáš ; Svoboda, Petr (advisor) ; Pergner, Jiří (referee)
Molluscs form the second largest animal phylum and are of great biological and economic significance. Their distinct evolutionary adaptations enabled them to inhabit a broad range of environments, with many of them invading new areas and becoming invasive pest species. Despite their importance, molluscan model systems have not received attention they deserve. In this bachelor thesis, I have reviewed the current state of molluscan model systems in molecular biology and analyzed their significance for more common use. From available data, it is apparent that the already established molluscan models are either marine or fresh-water, and therefore require more complex logistics and maintenance in order to set up a laboratory culture. To remedy the problem of aquaculture, the use of terrestrial gastropods was proposed. Here, I suggest that gastropods genus Deroceras have a good potential to become a new prominent molluscan model system in molecular biology.
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Quantitative Analysis of Gene Ancestry in Euglenoidea
Soukal, Petr ; Hampl, Vladimír (advisor) ; Burki, Fabien (referee) ; Horák, Aleš (referee)
Genes, units of genetic information, are passed from one individual to another, typically within the same species from parents to offspring. Occasionally, genes can be transferred to different species through a process called horizontal gene transfer (HGT). Endosymbiosis is a process in which one organism engulfs another organism and the genes flow between the two symbionts in a process called endosymbiotic gene transfer (EGT), which is a subtype of HGT. Eventually, the endosymbiont may become an organelle such as a mitochondrion or a plastid. Euglenids (Euglenoidea) are unicellular eukaryotes with diverse modes of nutrition - phagotro- phy (e. g., Peranema), osmotrophy (e. g., Rhabdomonas), mixotrophy (phagotrophy and phototrophy in Rapaza), and phototrophy (possessing plastids; e. g., Eutreptiella). The history of endosymbioses of green algae (especially Chlorophyta) and ancestors of Euglenophyceae (including Rapaza) is complex. In my thesis, I performed the quantitative analysis of gene ancestry (QAGA) based on transcripto- mic data of Euglena gracilis showing contribution of closely related Kinetoplastea (1,420 genes, 3.88 % of transcripts inherited vertically), and contribution of multiple "unrelated" (mainly) phototrophic organisms, e. g. Viridiplantae (572, 1.57 %), or Haptophyta (234, 0.64...
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Genomy chromeridních řas
MICHÁLEK, Jan
This work is mainly focused on the annotation of genomes of an important group of alveolate algae, which are the closest known phototrophic relatives of sporozoan parasites. The analysis is aimed to annotate their mitochondrial and nuclear genomes and search for biosynthetic pathways essential for sporozoans by combining the in-silico approach with supportive experiments. The initial study describes mitochondrial genomes of Chromera velia and Vitrella brassicaformis and models their unprecedently divergent respiratory chains. The following study summarizes the general characteristics of nuclear genomes of the two chromerids, highlights main genomic features shared with apicomplexan parasites, and traces the evolutionary transitions from the phototrophic ancestor to the obligate apicomplexan parasites. The study was completed by a comprehensive biochemical, genetic, and evolutionary analyses of fatty acid biosynthesis in chromerids.
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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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Operon structures inference in genome-wide analysis
Nejezchlebová, Julie ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor thesis is devoted to the problem of derivation of operon structures and creation of a software tool that allows prediction of operon structures. The tool both predicts operons based on gene expression information, but also refines already predicted operons with gene expression information. The tool is tested on the bacteria Escherichia coli BW25113 and Clostridium beijerinckii NRRL B-598. The theoretical part is devoted to description of operon structure and function, genome sequencing, transcriptome analysis, Clostridium beijerinckii NRRL B-598, Escherichia coli BW25113 and already available online tools for inferring operon structures. In the practical part of the thesis, the pre-processing of raw transcriptomic data to obtain a suitable format for the prediction of operon structures, testing of online tools and the actual implementation of the tool itself are discussed.
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Evolution of karyotypes and sex determination in the turtle family Geoemydidae
Clemente, Lorenzo ; Rovatsos, Michail (advisor) ; Montiel Jimenez, Eugenia Elisabet (referee) ; Castiglia, Riccardo (referee)
(IN ENGLISH) The majority of studied turtles show temperature-dependent sex determination, but genotypic sex determination (i.e. presence of sex chromosomes) was identified sporadically. This thesis aims to investigate and expand our knowledge on the evolution of the karyotype and the sex determination in turtles, particularly focusing on the family Geoemydidae, a group of turtles with previously documented variability in sex determination systems. The presence of sex chromosomes was explored by a combination of conventional and molecular cytogenetic techniques for the analysis of karyotypes, distribution of constitutive heterochromatin (C-banding) and repetitive elements and comparative genome hybridization (FISH, CGH). In total, 49 species of turtles from nine different families were cytogenetically examined in this study. In the family Geoemydidae, a remarkable similarity in karyotypes was identified, consisting of 2n=52 chromosomes (which is suggested to be the ancestral diploid number for all turtles) and a similar topology of rDNA loci and telomeric repeats. Sharma et al. (1975) previously reported ZZ/ZW sex chromosomes in Pangshura smithii. However, in the analysis presented in this thesis, it is suggested a possible misidentification of these sex chromosomes due to erroneous pairing of...
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Genome size evolution in the Zingiberaceae
Pospíšilová, Monika ; Fér, Tomáš (advisor) ; Kolář, Filip (referee)
The purpose of this study is to evaluate the existing knowledge on the evolution of genome size and also to focus on genome in the phylogenetic context. Among angiosperms we find a wide range of C-values (1C = 0.63 pg ? 1C = 127.4 pg), but the modal value is 0.6 pg. We still do not know much about the nature and mechanisms of plant genome size evolution, but we are learning more and more every year. There are already dozens of studies dealing with the dynamics of genome size of smaller taxonomic groups and on four of these they demonstrate possible approaches. Researching within higher taxonomic groups such as families is difficult and so more valuable. New research on the evolution of genome size in the family Zingiberaceae has started and my master thesis dealing with the Globbeae tribe should be part of it.
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