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Circulating tumor DNA in urine and its use as a potential biomarker of colorectal cancer
Surkovová, Veronika ; Ptáčková, Renata (advisor) ; Dračínská, Helena (referee)
Colorectal cancer (CRC) is a serious disease whose incidence has been steadily increasing. There is a high chance of cure and a good quality of life, if the treatment is started in the early stages of this disease. The so-called liquid biopsy, in which biomarkers from various body fluids are obtained and analyzed, could help with early detection of the disease, monitoring of the patient's condition and appropriate determination of the diagnosis. The aim of this study is to isolate and analyse circulating tumor DNA (ctDNA) from the urine of patients with advanced CRC. In these patients the ctDNA was detected in plasma. The method used for analysis is based on the principle of PCR with the formation of heteroduplexes, followed by the separation of "wild type" and mutated DNA fragments by denaturing capillary electrophoresis. Unlike plasma samples, the presence of KRAS mutations was not confirmed in urine samples. Neither the established procedure for plasma analysis, the attempt to enrich ctDNA by so-called purification, nor other tested isolation kits using the selected detection method allowed detection of the KRAS mutation in urine via ctDNA. Although urine ctDNA testing in general appears to be a promising method for improving the treatment level of (colorectal) cancer, and although its use could...
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Genetic factors in the etiology of sleep disorders
Dvořáková, Markéta ; Šolc, Roman (advisor) ; Červená, Kateřina (referee)
Sleep disorders are a group of disorders affecting a considerable part of proportion of the human population. Their aetiology is usually very complex and includes environmental and genetic factors. The nature of these disorders is often multifactorial. Sleep medicine and the field of synthesis of its findings with those of modern or classical genetics still offer quite a huge possibilities of research. However, despite many unresponsed questions, it is now possible to summarise the identified confirmed or suspected genes whose mutations are involved in the causes of these disorders. It is possible to estimate the heritability of certain disorders based on their multiple occurrence in families, presence in twins or prevalence in the population across different ethnics. This bachelor thesis focuses on genetic aspects in the etiology of sleep disorders, their heritability, the strength of the genetic component, and genetic links between some of the disorders.
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Circularly polarized antenna optimization
Niederle, Vojtěch ; Poměnková, Jitka (referee) ; Kadlec, Petr (advisor)
Tato práce se zabývá optimalizací pomocí Gaussových procesů, algoritmu diferenciální evoluce a její implementací v prostředí MATLAB. Teoretická část se zabývá tématem Gaussových procesů z hlediska matematické reprezentace, volby jádra, parametrů, matematických postupů pro implementaci, algoritmem diferenciální evoluce, mutací, křížením a teorií kruhově polarizovaných antén. Praktická část popisuje implementaci v prostředí MATLAB a zabývá se testováním tohoto algoritmu na testovacích funkcích. Výsledky jsou pak porovnány s jinými stochastickými optimalizačními algoritmy a je diskutována efektivita metody pro různé typy problémů. Na základě výsledků je metoda rozšířena o algoritmus diferenciální evoluce a je provedena optimalizace kruhově polarizované antény. Navržená anténa je vyrobena a změřena, výsledky jsou porovnány se simulacemi.
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Characterization of pore opening relevant residues in TM3 and TM4 domains of Orai1
ANDOVA, Ana-Marija
Calcium (Ca2+) ions play a crucial role in almost every aspect of cellular life. The most prominent calcium entry pathway into the cell is the calcium release-activated calcium (CRAC) channel, composed of the Orai1 protein, and the stromal interaction molecule STIM1. The channel is activated through conformational changes upon STIM1 coupling to the C-terminus of Orai1 protein following store depletion, which in turn allows Ca2+ influx into the cell. The abnormal function of the CRAC channel caused by mutations gives rise to distinct pathologies. Since it has not yet been elucidated how the signal propagation moves to the pore upon coupling, this thesis dives into its investigation by focusing on characterizing the TM3 and TM4 domains and their importance in leading to an open permissive conformation of the channel. The pivotal foundation for the creation of novel strategies in the modulation of the Orai1 function lies with the understanding of the dynamics of the Orai1 pore opening.
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Phylogenetic analysis and molecular detection of coronaviruses
MARHOUNOVÁ, Lucie
The aim of this bachelor thesis was to get acquainted with the creation of phylogenetic trees, which describe the relationships between coronaviruses and compare and assess the suitability of used and designed primers for the detection of a new type of coronavirus SARS-CoV-2. According to phylogenetic trees, it is possible to determine the evolutionary relationship of the studied organisms, which during evolution are subject to changes in their sequences, so-called mutations. These changes determine their development. The theoretical part of the bachelor thesis was focused on general acquaintance with viruses and subsequently coronaviruses and a new type of coronavirus SARS-CoV-2. SARS-CoV-2 has posed and continues to pose a major threat to the world. Furthermore, the issue of phylogenetics and finally the PCR detection method were discussed. In the practical part, phylogenetic trees were created using the computer program MEGA-X using the Neighbor-Joining method, which examined the phylogenetic relationships between coronaviruses focused mainly on SARS-CoV-2. The nearest coronaviruses of this new type of SARS-CoV-2 coronavirus were further compared using special BLAST software, which reported the percent agreement of the studied sequences. During these analyzes, SARS-CoV-2 was found to be most like the bat coronavirus RaTG13. Primers that are commonly used to detect SARS-CoV-2 are not disclosed, therefore primers from the CoVrimer web application have been used, where primers that have been used for scientific research are available. These were compared with the primers designed by the author. The design was performed as part of a bachelor's thesis using a special application Pirmer-BLAST. The primers obtained from the CoVrimer application were not designed to comprehensively distinguish all SARS-CoV-2 variants studied.
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Traditional plant breeding,advanced biotechnological engineering with emphasis on GM crops and environmental risk assessment of GMs
KOPICOVÁ, Klára
While searching for the best approach that would ensure an adequate supplement of the current still growing world population, the national governments support different strategies to multiply crop production and to stabilize profits. It is obvious that traditional plant breeding techniques are not capable to meet this challenge. Hence, scientists developed an advanced plant breeding techniques that cope with the adversity of the environment (e. g. pest and weed pressure, drought, salinity) as well as satisfy major needs of human society (e. g. sufficient yields, nutrient content). However, advanced bioengineering arouses distrust in consumers. This review compares both, the advanced plant breeding techniques with traditional breeding approaches; and the debate is further extended by critical assessment. Further focusing on genetic modifications (GMs) and genetically modified (GM) crops, this study describes a status of their growing on the example of two completely different strategies - strategy of the United States (U.S.) and the European Union (EU). Additionally, this thesis suggests a new design for testing of GM crops environmental risk assessment (ERA) - more precisely, a very little explored, potential transfer of GM gene constructs into invertebrates.
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Genetic basis of phenotypic variability in domesticated animals
Majerová, Veronika ; Reifová, Radka (advisor) ; Komárek, Stanislav (referee)
Understanding the mechanisms responsible for the origin of morphological variability among different species of animals represents an important goal in evolutionary biology. Origin and changes of the phenotypic variability during the evolution is possible to study in domesticated animals. The domesticated species of animals represent a brilliant model for studying the molecular mechanisms responsible for origin of new phenotypes due to enormous morphological variability of different domesticated breeds, effortless breeding in captivity and frequent knowledge of the genomic sequence. The aim of this bachelor work is to summarize actual findings about concrete mutations which are responsible for the origination of the new morphological characters in the domesticated animals. These findings can help us to clarify how the evolution functions on the molecular level.
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Thyroid tumors and their molecular genetic causes.
Šmídová, Barbora ; Dvořáková, Šárka (advisor) ; Soták, Matúš (referee)
The aim of this work is to summarize actual literature overview and to collect the up- to-date knowledge on genetic causes of the development of thyroid carcinomas. Thyroid carcinomas represent the most often endocrine malignancy and its incidence is still growing. This work describes all types of thyroid carcinomas derived from different cell types and are distinguished also according to the degree of differentiation. The main genetic changes in the tumor tissues of the medullary, papillary, follicular and anaplastic thyroid carcinoma are described. Thyroid carcinomas occur mostly in sporadic form, rarely as a familial disease. The causes of familial forms of thyroid carcinomas are also summarized and the main mutations in the germ-line DNA are identified. Key words: carcinoma, genetics, mutation, thyroid
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Optimization of proces for detection of free tumor DNA in plasma and its clinical utility for colorectal cancer, lung cancer and pancreatic cancer patients
Belšánová, Barbora ; Benešová, Lucie (advisor) ; Tachezy, Ruth (referee)
In current days, examination of circulating tumor DNA (ctDNA) finds new use across different cancers. It is directed at tumor-derived short fragments of DNA present in peripheral blood of patiens (mainly in advanced stages). Due to its minimal invasivity, almost 100 % specificity and relatively high sensitivity in stage IV patients, this approch found its main potential clinical utility especially in early detection of disease relapse or progression after tumor resection (i.e. post-operative follow-up), prediction and monitoring of therapy response and estimation of prognosis. As a result of minute levels of ctDNA on a high background of other non-tumor DNA fragments present in plasma, a suitable method exhibiting highest sensitivity is the key for proper detection of this marker. The approach is predominantly based on initial identification of a mutation in tumor tissue and its subsequent detection in plasma. The present work is aimed at optimization of ctDNA isolation and method of its detection based on PCR amplification followed by heteroduplex analysis by denaturing capillary electrophoresis (DCE) to achieve highest sensitivity for detection of mutated fraction in plasma sample. I have applied the optimized protocol to examine ctDNA in three types of cancers, namely colorectal cancer (122...
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Trombophilic states during pregnancy
Košatová, Andrea ; Ehler, Edvard (advisor) ; Pavlasová, Lenka (referee)
The aim of this thesis is to summarize the available data concerning the influence of trombophilic states on the process of pregnancy and to present the results obtained by investigating the prevalence of congenital trombophilia in infertile women and its influence on the success rate of assisted reproduction. It is aimed at those interested in the problematics - be it professionals, medical students or women planning pregnancy or cannot get pregnant. The theoretical part draws data from literature written by leading Czech experts in the field and from scientific journals, included are also foreign sources. The practical part was executed with the kind permission of the PRONATAL s.r.o. centre for assisted reproduction. Key words: venous thromboembolism, trombophilia, trombophylaxis, gravidity, mutation, screening
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