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Identification of Organisms Based on Analysis of Nucleotide Density Vectors
Maděránková, Denisa ; Babula, Petr (referee) ; Schwarz, Daniel (referee) ; Provazník, Ivo (advisor)
Most methods for analysis of genomic data work with symbolic sequences. Numerically represented genomic sequences can be analyzed by signal processing methods. A new method of numerical representation of DNA sequences, nucleotide density vectors, is proposed in this thesis. Usability of this method for purposes of molecular species identification is tested on DNA barcoding sequences. DNA barcoding is modern and popular methodology based on comparison of short mitochondrial DNA sequences. Beside species identification by proposed method based on nucleotide density vectors, higher taxa rank identification (e.g. families) was also tested. Furthermore, dendrograms were constructed from standardly used evolutionary distances and distances between nucleotide density vectors and the dendrograms were compared.
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Analysis of selected gene variants in athletes - runners at 400 m
Šplíchalová, Dominika ; Petr, Miroslav (advisor) ; Šteffl, Michal (referee)
Title: Analysis of selected gene variants in athletes - runners at 400 m Objectives: This work aims to find out what the genetic profile of athletes - runners at 400 meters, who are working in lactate mode, looks like. Methods: A cross-sectional investigation involved 203 East European Caucasian males and was conducted collaboratively at the FTVS UK and Józef Piłsudski University of Physical Education in Warsaw (AWF Warsaw). The athletes, after a brief warm- up, participated in a single 30-second Wingate test. DNA samples were collected non-invasively through saliva swabs. Lactate levels were measured using an invasive approach. Results: In the polymorphisms rs4646994 gene ACE was found to have a significant difference in genotypic (p = 0.001, x2 = 14.90) and allelic (p = 0.004, x2 = 8.52) frequencies between the overall athlete group and the controls. A notable difference in the ACE gene showed the comparison of the genotypes (p = 0.001, x2 = 13.66) and between the alleles (p = 0.003, x2 = 8.89) between the control group and elite athletes. The last statistically significant difference was observed among the genotypes (p = 0.03, x2 = 6.79) between the sub-elite athletes and the control group. When assessing the genotypic and allelic frequencies for the polymorphisms rs1815739 in the ACTN3 gene, we...
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Speciation genomics in nightingales
Mořkovský, Libor ; Reifová, Radka (advisor) ; Macholán, Miloš (referee) ; Piálek, Lubomír (referee)
Speciationisusuallyaslowprocessoccurringoverthousandstomillionsofyears.Thismakes speciation research difficult because no direct observation or manipulation is possible. At best, we can gain some insight by inferring the population history and structure in very fine detail by investigating genetic markers in multiple individuals of the nascent species. Today, speciationresearchisinanunprecedentedpositionthankstotheadventofhigh-throughput sequencingmethods,whichmakeiteasier and cheaper than ever before to evaluate multiple markers in many individuals. Speciation is not a straightforward process that happens in the same way every time, but rather a phenomenon occurring when genetic and ecological circumstancesactinginsymphonyultimatelyleadtoreproductiveisolationoftwosubpopula- tions. This is why it is important to study multiple model systems to understand the general principles behind speciation. We worked with two species of nightingales (Luscinia luscinia andL.megarhynchos)thatdivergedapproximately1.8Mya,likelyduetoglacialfluctuations in Europe. Our main goal was to use these new high-throughput sequencing methods to (1) detect interspecific hybrids between the species, (2) estimate levels of interspecific gene flow,(3)findareasofthenightingalegenomethatunderliereproductiveisolationand,finally, (4)...
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Surface phenotype of human carcinoma cancer stem cells (CSC)
Bočková, Marie ; Drbal, Karel (advisor) ; Čermák, Vladimír (referee)
Tumor is composed of a heterogenous mass of cells. Similar to normal healthy organs and tissues, these can be divided into individual cellular subpopulations according to morphology, function and expression patterns. A subpopulation of cells that are able to give rise to all of these cellular lineages is referred to as cancer stem cells (CSC). CSCs have the capabilities of normal stem cells such as the self-renewal and the ability to give rise to a heterogenous population of differentiated cells. Usually, this is the most resistant subpopulation within a tumor, highly non-responsive to therapy. Doing so, they are the cause of residual disease. Characterisation of CSC markers of individual tumor types is beneficial since it enables higher therapy efficacy via targeting this cell population. The -omics approaches to characterisation of the surface proteome bring a broader view into the field when searching for a unique gene signature of specific cancer stem cell types. It has been found that these cells can be identified based on the high expression levels of CD44, CD90 and CD49f. Among other markers, CD47 is an important marker for its immunosuppressive function.
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Genomic approach in speciation studies
Habalová, Kateřina ; Hulva, Pavel (advisor) ; Mikulíček, Peter (referee)
Speciation, adaptation and hybridization are three concepts, each one referring to different process but having a common evolutionary context. Maternal line splits into two sister lines or only one line cleaves from maternal one during speciation. However it leads to formation of new species. Adaptation and hybridization can lead to formation of new species as well. New species arise by adapting to new conditions during adaptation. Within hybridization it is a desecendant of two different lines mating amongst themselves. Most of this thesis is being addressed to these issues, the lesser part is addressed to specific examples. The chapter about next-generation sequencing methods is also included, as these methods have been used more frequently recently. Key words: speciation, adaptation, hybridization, genomics, next-generation sequencing
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Implemenation of the RAD sequencing methods to the population genetic studies of hedgehogs from the genus Erinaceus
Loudová, Miroslava ; Černá Bolfíková, Barbora (advisor) ; Choleva, Lukáš (referee)
Hedgehogs from the genus Erinaceus are an important model organism for studying the postglacial recolonisation of Europe and the processes that take place in the secondary contact zones of their areas of distribution. In this study, five individuals of white-breasted hedgehog (Erinaceus roumanicus), four individuals of western hedgehog (Erinaceus europaeus) and one estimated hybrid were analysed. Geographical distribution of individuals used in the study covers the region of the Central Europe, however in the further research expansion of analsysed individuals will be needed and the whole Palearct should be sampled. The main goal was to implement novel methods in research of hedgehogs, which will enable to map the population-genomic structure of the genus Erinaceus in western Palearct. The method RADSeq (Restriction site associated DNA sequencing) enables to obtain polymorphic markers, e.g., SNPs which we used (Single Nucleotide Polymorphisms) across the genome. In this work it was analyzed 16382 SNPs. Using the binary data which indicates the presence and absence of SNPs for each species, hypotheses raised under classical analyzes of genetic markers from previous studies have not been fully confirmed. In further research it will be necessary to verify possible occurrence of biases connected with...
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Speciation genomics in nightingales
Mořkovský, Libor
Speciationisusuallyaslowprocessoccurringoverthousandstomillionsofyears.Thismakes speciation research difficult because no direct observation or manipulation is possible. At best, we can gain some insight by inferring the population history and structure in very fine detail by investigating genetic markers in multiple individuals of the nascent species. Today, speciationresearchisinanunprecedentedpositionthankstotheadventofhigh-throughput sequencingmethods,whichmakeiteasier and cheaper than ever before to evaluate multiple markers in many individuals. Speciation is not a straightforward process that happens in the same way every time, but rather a phenomenon occurring when genetic and ecological circumstancesactinginsymphonyultimatelyleadtoreproductiveisolationoftwosubpopula- tions. This is why it is important to study multiple model systems to understand the general principles behind speciation. We worked with two species of nightingales (Luscinia luscinia andL.megarhynchos)thatdivergedapproximately1.8Mya,likelyduetoglacialfluctuations in Europe. Our main goal was to use these new high-throughput sequencing methods to (1) detect interspecific hybrids between the species, (2) estimate levels of interspecific gene flow,(3)findareasofthenightingalegenomethatunderliereproductiveisolationand,finally, (4)...
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Genome Assembly and Annotation of Biparental Bee Ceratina nigrolabiata
Fraňková, Tereza ; Straka, Jakub (advisor) ; Kolísko, Martin (referee)
Biparental care in Hymenoptera is a little studied behaviour. This kind of parental care was discovered and the ethological aspect described in the bee Ceratina nigrolabiata from the Czech Republic and is well understood on the ethological level. However, biparental care is not a common behaviour and the lack of genomic studies of this behaviour complicates the understanding of the origin of the biparental care and its underlying pathways on the genomic and physiological level. This master's thesis presents the genome analyses of a biparental bee Ceratina nigrolabiata. It consists of a brief summary of the known parental behaviour across insects, characteristics of the genus Ceratina, summary of the used genomic methods and presents a candidate genes for the transcriptomic study of the biparental behaviour of Ceratina nigrolabiata. Key words: biparental care, genomics, Hymenoptera, Insecta, Ceratina, small carpenter bees
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Construction and quality assessment of the genome assemblies
Korená, Lucie ; Leontovyč, Roman (advisor) ; Vorel, Jiří (referee)
Detailed information of the genome of the studied organism is crucial for many fields of modern research. Actual sequencing technologies are not able to read the whole DNA molecule at once therefore only fragments of the genetic information are obtained, which are not sufficiently informative on their own. The goal of the genomic-bioinformatic approach is to assemble these fragments into complete original information - genome assembly. The process of the genome assembly is demanding in terms of computational power, software equipment and expert staff. Many assemblers - programs for genome assembly are available differing in performance, size of the analyzed genome or target organism. The quality of final assembly is fully dependent on assembler and setting of inner parameters. In practice, multiple assemblies are constructed and their quality evaluated according to the technical and biological parameters. The presented thesis describes current high throughput sequencing technologies, different approaches and algorithms for genome assembly and methodology for their quality assessment. The practical part is focused on assembly and its quality assessment using Illumina data of the bird fluke Trichobilharzia szidati.
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