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Machine learning models for quantifying phenotypic signatures of cancer cells based on transcriptomic and epigenomic data
Koban, Martin ; PhD, Florian Halbritter, (referee) ; Mehnen, Lars (advisor)
S rozvojom techník pre efektívnu akvizíciu genomických dát sa jednou z kľúčových vedeckých výziev stala interpretácia výsledkov týchto experimentov v zmysluplnom biologickom kontexte. Táto práca sa zameriava na využitie informácií ukrytých v dobre charakterizovaných transkriptomických a epigenomických dátach z verejne dostupných zdrojov pre účely takejto interpretácie. Najskôr je vytvorený integrovaný súbor dát generovaných metódami DNase-seq a ATAC-seq, ktoré kvantifikujú chromatínovú dostupnosť. Tieto údaje sú doplnené verejne dostupnými výsledkami techniky RNA-seq pre kvantitatívne hodnotenie génovej expresie a vhodne predspracované pre ďalšiu analýzu. Pripravené dáta sú následne použité na trénovanie modelov strojového učenia (klasifikátorov) s dvomi základnými cieľmi. Po prvé za účelom augmentácie metadát prislúchajúcich k jednotlivým biologickým vzorkám v trénovacom dátovom súbore pomocou predikcie nedefinovaných anotácií. Po druhé pre anotáciu zle charakterizovaných testovacích dát (nepoužitých v trénovacej fáze) za účelom overenia generalizačnej schopnosti zostavených modelov. Dosiahnuté výsledky ukazujú, že natrénované klasifikátory sú schopné zachytiť biologicky relevantné informácie, zatiaľ čo vplyv technických artefaktov je minimalizovaný. Navrhnutý prístup je preto schopný prispieť k lepšiemu pochopeniu komplexných transkriptomických a epigenomických dát, predovšetkým v oblasti onkologického výskumu.
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Natural drugs in cancer treatment and their cytotoxicity
Hájková, Tereza ; Raudenská, Martina (referee) ; Provazník, Ivo (advisor)
The thesis deals with the natural substances in context with the cancer disease. The natural substances have a positive effect on the human organism and they are able to influence the viability and the growth of the cancer cells. The main mechanical device is to influence the mechanisms needed to start the apoptosis of the cancer cells and stopping further proliferation. The cancer cell lines utilization in the cancer disease is discussed in the thesis too. The thesis states common methods of determining the natural substances cytotoxicity. For the experimental part of the thesis it was chosen the MTT test method and the xCELLigence system for monitoring in real time. The mechanical device of the tested substance capsaicin in application on the prostate cell lines, tumorous PC3 and nontumorous PNT1A influence will be observed within the experimental part of the thesis.
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Analysis of NGS data for study of transposon activity in cancer cells
Hrazdilová, Ivana ; Čegan,, Radim (referee) ; Eduard, Kejnovský (advisor)
Theoretical part of this diploma thesis gives a brief characteristic of human mobile elements (transposons), which represents nearly 50% of human genome. It provides basic transposon clasification and describes types of transposons present in hunam genome, as well as mobilization, activation and regulation mechanisms. The work also deals with the domestication of transposons, describes the ways in which TE contribute to DNA damage and summarizes the diseases caused by mutagenic activity of transposons in the human genome. Conclusion of theoretical part describes next-generation sequencing technologies (NGS). As practical part, data from RNA-seq experimet were analyzed in order to compare differen transposon activity in normal and cancer cells from prostate and colorectal tissues. As like as publicly available sophisticated tools (TopHat), new scripts were created to analyze these data. The results show that cancer cells exhibit overexpression of transposons. This corresponds with the published results and suggests a connection of transposon activation with cancer development.
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Native hyaluronan as a delivery system for hydrophobic drugs
Černá, Eva ; Mravec, Filip (referee) ; Pekař, Miloslav (advisor)
The aim of this paper is to discover whether it is possible to use the native form of hyaluronic acid as a hydrophobic drug carrier for a targeted distribution in the body. In its structure, hyaluronic acid is a linear high molecular weight biopolysaccharide which is found in most living organisms. Hyaluronan is involved in many physiological processes and therefore is essential for the functionality of the human body. It is in most tissues of the human body, high concentration is in the skin, the vitreous body and is also observed in cancer cells that contain several receptors for hyaluronan. These receptors include CD44 and RHAMM. The interaction of the hyaluronic acid delivery system and the hydrophobic medicinal with these receptors could ensure a free passage for drugs to the affected tissue, where the release of the drug would destroy the affected cells. The drug would directly target the damaged tissue and did not burden the rest of the body like the cytotoxic agents do. In this paper the native form of hyaluronic acid, which we normally find in the human organism, was chosen as the carrier. Its properties do not stand above other carrier systems, but its biocompatibility and biodegradability in the body greatly exceed them. High molecular weight hyaluronic acid was used as a carrier and the hydrophobic dye sudan red G, a substance of similar properties, was used instead of a hydrophobic drug.
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Detection of Pt derivatives using ICP mass spectrometry
Zelinová, Karin ; Hložková, Michaela (referee) ; Vašinová Galiová, Michaela (advisor)
This Bachelor´s thesis deals with the monitoring of chemotherapeutic penetration into tumor cells. Due to the toxicity of drugs, targeting them is absolutely essential from the point of view of minimizing the interference with healthy tissue of the patient. In order to achieve the best possible targeting, it is necessary to monitor the penetration of chemotherapeutics into cells. The subject of study was platinum-based drugs therefore the ICP-MS method was chosen to analyse the drug content in cells, because it is suitable for fast and reliable detection of trace amounts of elements. The theoretical part of the Bachelor´s thesis focuses on the description of ICP-MS, as a method, which was chosen for the detection of platinum derivates. It also summarizes the use of platinum-based drugs in cancer therapy. The practical part of the thesis deals with the analysis of cells exposed to platinum-based chemotherapeutics. Detection and quantification of platinum in the cells were determined by both SN-ICP-MS and LA-ICP-MS. To verify the results, the analysis of the solution was also performed by the AAS method. The results show, that the drug was most readily taken up by A2780 cells. It was also shown that cisplatin was the most accumulated drug.
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Centre for Prevention, Masaryk Oncology Institute in Brno
Buzová, Magdaléna ; Kraus, David (referee) ; Galeová, Nicol (advisor)
The objective of the diploma thesis is the new building of Cancer Prevention Centre, first of its kind in the Czech Republic. The site is located on steep terrain of the south hillside of Žlutý kopec in Brno, which is a part of Masaryk Oncological Hospital complex. The aim of the Cancer Prevention Centre is to attract the citizens’ attention and invite them to undergo a preventive medical check-up with the potential to save hundreds of lives every year. The project takes this fact in consideration and strives to find ways leading not only towards establishing new relationship between the building and the public, but also towards connecting the city centre and nearby by residential area with the hospital complex. The three volumes of the buildings create a dynamic composition and therefore complete the characteristic development of Masaryk Oncological Centre. The main concept however revolves around the motive of instability, balance and journey which are all linked to tumour diseases.
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P53 protein isoforms production and purification in the bacterial expression system
Vadovičová, Natália ; Obruča, Stanislav (referee) ; Brázda, Václav (advisor)
Apart from the p53 protein, the TP53 tumor-suppressor gene is expressed as another eleven protein isoforms with the use of alternative splicing, alternative promotors and alternative translational initiation sites. Abnormal expression of these isoforms has been observed in tumor tissues. The binding properties as well as the biological functions are also modulated, due to sequential and therefore structural differences from the p53 protein. p53 is regulated by these isoforms in both suppressive and supportive manner. Explanation of the p53 isoform regulation mechanism in cells could lead to desired alternative splicing of the chosen isoforms, and modulation of isoform expression could be used in cancer treatment based on p53 therapy. Basic information about p53 protein is summarised in the theoretical part of this master thesis, supplemented with recent advances in the field of p53 isoforms, as well as the Gateway cloning method. The main goal of the experimental part was p53 isoform production in a bacterial expression system. Prior to the protein production, DNA sequences coding twelve p53 isoforms were prepared using PCR and Gateway cloning. In total, twelve entry clones and eight expression clones were prepared by cloning the isoforms’ sequences. After the protein production and purification, the detection using SDS-PAGE and Western Blotting was performed with five p53 protein isoforms: p53, 40p53, 40p53 and 40p53. DNA binding properties of p53 protein isoforms will be tested in subsequent research.
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Hyaluronan for targeted drug delivery
Ureš, Tomáš ; Vávrová, Milada (referee) ; Pekař, Miloslav (advisor)
Hyaluronic acid (hyaluronan, HA) is a linear polysaccharide formed from disacharide units containing N-acetyl-D-glucosamine and glucuronic acid. HA is present in almost all biological fluids and tissues. In many cancer cells there is an upregulation of CD44, a receptor that binds HA. The receptor CD44 collocates hyaluronan in the special way. The bioconjugates built-up from the cytotoxic substances and hyaluronan are called prodrugs. The prodrugs can be used for targeted drug delivery system. Their main advantage is there is no need to medicine so high doses of pharmaceuticals and their adverse side effects are minimized. Hyaluronan can be used as well as the intra-articulation injection by osteoarthritis. HA is also used as the nutrition of joints, by treatment for diverse dermatic lesions, the repair of scars and it can be the ingredient of eye drops and nasal sprays. The cosmetic manufactures add HA into anti-wrinkle creams and anti-aging care.
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Measurement of antioxidant markers at children with malignant tumours
Hořavová, Lenka ; Masařík, Michal (referee) ; Provazník, Ivo (advisor)
Tumour disease belongs to one of the most serious health problems of our time. Finding of new indicators to recognise the beginning of the illness is the key role for today‘s research. Oxidative stress is known to be related to the disharmony between the prooxidant concentration and antioxidant mechanisms. Moreover, it is shown that these changes are very important for patients. Further it appears that these changes are very significant with path physiologically critically ill patients. Direct measuring of the reactive oxygen radicals or oxidative stress’ markers is still very hard in clinical medicine. The oxidative stress’ level is watched as the change of the antioxidant activity or alternatively as the antioxidant status. Work is focused on the spectrophotometric fixing of the antioxidant activity and markers signalising the damage of organism. The automated photometric analyzer is going to be used to gain the experimental data. Data will be processed statically.
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Influence of liposomal platinum cytostatics on cancer cells – voltammetric study
Laníková, Petra ; Prášek, Jan (referee) ; Hynek, David (advisor)
Aim of this thesis is voltammetric study influence of liposomal platinum cytostatics on cancer cells. One of the goals is summarize available informations about influence of cisplatine on cancer cells, its encapsulation into liposome and affection of this cytostatic cisplatin encapsulated in liposome on cancer cell lines. In literary recherche is detail description of these issues. Than is there specification of voltammetric methods, which serve to electrochemical detection of cisplatin. Based on literary recherche was chosen the best method for detection and subsequently the method was optimalized and than was applied to measuring itself.
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