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Bovinne papillomaviruses
Voběrková, Eva ; Drda Morávková, Alena (advisor) ; Kuthan, Martin (referee)
Bovine papillomaviruses (BPV) are small nonenveloped dsDNA viruses belong to the family Papillomaviridae. One of the characters of this family is strong species and tissue specificity, but some BPVs are represent an exception and they are able to infecting other groups of vertebrates. However transmission on human has not been proved yet. All viruses from this groups, including BPV have considerable tumorigenic potential, in particular for the infection non-permissive cells. In the natural host, they are causing clinical disease, which manifest papillomas, that may interfere with host of life what cause considerable economic loss. BPV served as model organisms for study. Papillomavirus family and these findings helps understand their human counterparts (human papillomaviruses, HPV). Recently, studies of BPV are not so frequent, overshadowed the success of vaccines against HPV. To the other hand, this success is encouradged for as to develop the similar vaccines against BPV order to avoid disease of farm animals. The successful development working on such a vaccine, is needed understand function virus and viral proteins and mechanism their interaction with the host cell. It is also necessary to map individual BPV their similarites and differences that to the specifics of each types. This work...
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Regulation of gene expression in anaerobic parasitic protist and practical application of knowledge
Brzoň, Ondřej ; Zubáčová, Zuzana (advisor) ; Horváthová, Lenka (referee)
Because of its importance for every single cell, regulation of gene expression is often studied at all levels today. On the other hand, rather sparse amount of information is available for protists and our understanding of their gene expression is nearly limited to several model organisms. Three anaerobic human parasites have been studied in details: Trichomonas vaginalis, Entamoeba histolytica and Giardia intestinalis. Most recently, some others anaerobic protists (e.g. Entamoeba invadens or some species of Spironucleus genus) have been researched as well. This work is focused on the structure of promoter regions in protein coding genes and application of this knowledge in construction of transfection systems as one of the most effective and powerful tools in molecular and cell biology.
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Changes in embryonal programing induced by diabetes mellitus
Landsmann, Lukáš ; Pavlínková, Gabriela (advisor) ; Tlapáková, Tereza (referee)
Embryonic development is sensitive to environmental changes. These changes may lead to changes in the embryonic programming. Changes in programming embryos can occur due to inadequate nutrition, stress, treatment with chemicals and also due to diabetes. Epigenome reacts sensitively to environmental factors regulating gene transcriptional activity. Changes in the epigenome lead to a changes in gene expression, which can have a negative impact on the physiology and metabolism of organism. Maternal diabetes may alter embryonic and fetal development and may result in diabetic embryopathy. Furthermore, maternal diabetic enviromental plays an important role in the predisposition of offspring to a number of chronic diseases later in life. The offspring of diabetic pregnancies demonstrate differences in metabolic, cardiovascular, and inflammatory variables, compared to the offspring of nondiabetic mothers. This thesis summarizes the genetic and epigenetic factors involved in the development of diabetic embryopathy and in the embryonic programming. Key words: Diabetes mellitus, diabetic embryopathy, transcriptional regulation, genetic and epigenetic factors , embryonic programming, genome
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Pozitive and negative selection of mitochondrial genome
Svoboda, Matěj ; Kupková, Kristýna (referee) ; Maděránková, Denisa (advisor)
The bachelor thesis engages with problematics of positive and negative selection of mitochondrial genome. Thesis is divided into two parts. First part grapples with theory and explanation of fundamental definitions, in particular understates mitochondrial genome, nucleotide mutation, positive and negative selection and furthermore evolution models. Second part focuses on processing mitochondrial DNA practically and on establishing functions in programming environment R. The emphasis is foremost on gene sequencing alignment and exploring substitutions. Consequently, obtained outcomes are contrasted with PAML and KaKs Calculator programme outcomes.
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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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Prediction of the replication origin in prokaryotic genomes
Lebó, Marko ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
This bachelor’s thesis deals with the problem of origin of replication (oriC) detection in genomes of prokaryotic organisms. It describes the differences in the processes of initiation of replication in organism of the both procaryotic domains – Bacteria and Archea. It describes the possibilities of conversion of DNA sequences into their numeric representaions and evaluates their application for oriC detection. Also, it describes different approaches in oriC detection and describes te functioning of already present programmes for oriC detection. Finally, it suggests a new tool for oriC detection in bacterial genomes – FindOri and discusses results, achieved during the testing of this tool.
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Současná úroveň poznání genomu druhu Prunus persica (L.) Baatsch.
Chaloupský, Pavel
Presented paper summarizes the status of knowledge on the peach (Prunus persica [L.] Batsch.) genome. Peach belongs to the Rosaceae family. This species is, along with other important crops, encompassed by Prunus genus. Peach is one of the least hardy fruit species. Despite that, it is widely cultivated in the temperate zone and has indisputable economic importance. Because of its importance and suitable properties, peach is genetically well characterized. Methods of molecular genetics have played a considerable role on the current state of knowledge on the peach genomics. Modern molecular methods may be utilized in order to identify and localize specific DNA sequences -- markers. Molecular markers are widely used for DNA fingerprinting, genome mapping, development of improved varieties and other applications.
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Comparison of genomes by synteny block analysis
Pavel, Tomáš ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
The theoretical part of this bachelor thesis is aimed at basics of genetics. Term of gene and mutation are introduced in this section. There are gene and chromosome mutations mentioned and described. Following section is devoted to comparative genomics and especially to synteny. There is described what the synteny actually is and how the synteny arises. The end of the theoretical part of this thesis is about the evolution and there are described ways of sorting permutation vectors. The practical part of this bachelor thesis includes description of developed software. Output of this software is a dot-plot which shows detected synteny blocks. Indexes of these blocks are listed in GUI. The second important output is number of permutation steps. This number determines evolutionary distance between two analysed DNA sequences. The very last section is aimed at analyse of synthetic and real DNA sequences.
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Digital signal processing of mitochondrial genomes
Sonnenschein, Jiří ; Vítek, Martin (referee) ; Škutková, Helena (advisor)
The aim of this thesis is to test new less hardware demanding method of mitochondrial genom classification, for which numerical representation of biological sequences is used. Introductory part is focused on description of nucleic acids and mitochondrion. In following part of thesis, types of numerical representation of biological sequences without losing the original biological information are described. There are introduced possibilities of phase and frequency-domain analysis and principles of cluster analysis and dendrogram construction methods. Practical part of this work deals with analysis of mitochondrial genome for which cumulated and unwrapped phases are calculated. Mitochondrial sequences are compared by cluster analysis and dendrogram is constructed.
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Identifying CpG islands in genomes of eukaryotes
Urbánková, Kateřina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with searching CpG islands in DNA. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There is basic information about human and chimpanzees genome and specification of CpG islands. Practical part consists of a program that searches for CpG islands in sequences, it displayes and saves it. This work includes analysis of genes which are common for Homo sapiens, Pan troglodytes, Mus musculus and Bos taurus.
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