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Effect of abacavir on the expression of nucleoside transporters, adenosine receptors, and enzymes involved in adenosine synthesis and biodegradation in trophoblasts
Gala, Viktor ; Červený, Lukáš (advisor) ; Čečková, Martina (referee)
Charles University in Prague Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Viktor Gala Supervisor: doc. PharmDr. Lukáš Červený, Ph.D. Title of diploma thesis: Effect of abacavir on the expression of nucleoside transporters, adenosine receptors, and enzymes involved in adenosine synthesis and biodegradation in trophoblasts The nucleoside reverse transcriptase inhibitor (NRTI) abacavir (ABC) is now the mainstay of combination antiretroviral therapy (cART) for HIV in pregnant women. The introduction of cART, along with several other measures, has reduced mother-to-fetus transmission of HIV to less than 1% in recent years. The placenta is a key organ for the health of both the fetus and the mother. Imbalances in placental development can result in adaptive changes and fetal programming errors. cART recommended in pregnancy is known for its good safety profile, but some epidemiological studies suggest a higher risk of reduced fetal weight, preterm birth, etc. The placenta is a rapidly growing organ dependent on the supply of building materials that resembles tumor growth in certain aspects. Nucleosides are promoters of tumor proliferation and are involved in the development of immunotolerance. The placenta is complexly equipped for nucleoside synthesis, uptake,...
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Evaluation of gene expression of selected ABC and SLC transporters in the HTR-8/SVneo cell line during stimulation with pro-inflammatory cytokines
Pokorná, Petra ; Čečková, Martina (advisor) ; Mladěnka, Přemysl (referee)
Charles University Faculty of Pharmacy in Hradec Králové Department of Pharmacology & Toxicology Student: Petra Pokorná Supervisor: Assoc. Prof. PharmDr. Martina Čečková, Ph.D. Consultant: Mgr. Simona Dudičová Title of diploma thesis: Evaluation of gene expression of selected ABC and OATP transporters in the HTR-8/SVneo cell line during stimulation with pro-inflammatory cytokines Placenta is the first and the largest fetal organ that gradually develops during pregnancy and plays an essential role in the development of the fetus. It fulfills the entire spectrum of functions, ensures the transport of nutrients to the fetus and the removal of waste substances back into the maternal circulation, protects the fetus from toxins, and at the same time fulfills a certain mechanical and especially immunological barrier between mother and fetus. One of the main functions of the placenta is the transport function which is made possible by membrane transporters present mainly in the syncytiotrophoblast layer of the placenta. Transporters in the human placenta can be divided into two families, SLC and ABC which are further divided into several subfamilies. The expression of transporters changes physiologically during pregnancy, but pathological conditions such as inflammation can also influence the expression....
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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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DNA Microarrays Data Analysis
Hebelka, Tomáš ; Jaša, Petr (referee) ; Burgetová, Ivana (advisor)
This work concerns with data analysis of DNA microarrays by using cluster analysis. It explains biological terms - gene expression and DNA microarray. Next, it contains mathematical and informatical description of clustering methods and describes a way to apply these methods to microarrays data. Next, the work contains implementation's detail of clustering methods k-means, DBSCAN and introduces an original clustering algorithm Strom++. Then, description of implementation and application manual follow. Finally, accomplished results are evaluated.
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Identification of non-coding RNAs of Clostridium beijerinckii NRRL B-598 using RNA-Seq data
Pomykalová, Barbora ; Sedlář, Karel (referee) ; Jurečková, Kateřina (advisor)
This bachelor thesis contains short introduction into bacterial small non-coding RNA problematic. It is oriented on their features and functions in organisms, especially in bacteria Clostridium beijerinckii NRRL B-598. Bachelor thesis also contains description of various laboratory methods for gene expression determination and suggests a detection method for small non-coding RNA in bacteria Clostridium beijerinckii NRRL B-598. Suggested method works with data, which were obtained by RNA-Seq technology. Within the framework of the bachelor thesis was suggested method implemented in programming and numeric computing platform MATLAB and its results were discussed.
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Study on gene expression in Cupriavidus necator and other selected polyhydroxyalkanoates producers
Centnerová, Radmila ; Šedrlová, Zuzana (referee) ; Pernicová, Iva (advisor)
The aim of this bachelor thesis was study on gene expression in bacterium Cupriavidus necator H16 that is known as a model bacterium for the metabolism of polyhydroxyalkanoates. In the first part of this thesis, the optimalization of RT-qPCR method was performed. The optimized method was implemented on the study on gene expression. Furthermore, there were tested several commercial isolation kits for the genomic DNA isolation, the RNA isolation and the reverse transcription of the RNA and synthesis of the complementary DNA. These kits were compared in order to choose the one that would have provided the most relevant results and also the kit handling would have been simple and safe. There were different results accomplished for all kits. This means the kit used for the isolation had unneglectable impact on the quality of the isolated nucleic acid and therefore also on the success of the whole measurement. Isolated genomic DNA was used for optimalization and calibration. Isolated RNA and complementary DNA were used in the second part of the thesis. In this part, the studied bacterium was cultivated under various conditions and carbon sources. Subsequently, the optimized RT-qPCR method was performed and used for study on gene expression of chosen genes involved in the biosynthesis of polyhydroxyalkanoates. There were more significant differences in gene expression observed for fructose as a carbon source, compared to -butyrolacton as a carbon source. The greatest increase of the gene expression for fructose as a carbon source was measured for gene encoding 4-hydroxyphenylacetate-3-hydroxylase. There were more considerable differences in gene expression observed for -butyrolacton as a carbon source only for gene encoding 4-hydroxybutyrate dehydrogenase. Therefore, the choice of the carbon source impacts fundamentally the gene expression.
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Nutrigenomics and diseases of civilisation
Sadel, Peter ; Souralová Popelková, Miriam (referee) ; Vránová, Dana (advisor)
The aim of the first part of this bachelor´s thesis is to explain and describe the basic terms which were used as diseases of civilisation, gen, genome, nutrigenomics, nutrigenetics. The second part of this work focuses on the characterization and description of some of the most often occurring diseases of civilisation in this world as obesity, diabetes mellitus or cardiovascular diseases and it has to point at possible causes of their formation and prevention. In the following chapters knowledge and practises of nutrigenomics were used during searching for the reasons of formation and prevention of civilisation diseases. Nutrigenomics is relatively a young discipline of science and only future research and monitoring will show its possible meaning in the future. The main goal of this work was to summarize and clearly demonstrate information about given theme from various information sources.
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Analysis of intron sequence variability
Kukačková, Hana ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This bachelor thesis reviews genetic expression, the main characteristics of introns, their importance, and the methodology of their recognition. Practical part focuses on intron variability analysis and conservative sequences searching. In the beginning, there is a structure of nucleic acids with their chemical and physical characteristics reviewed, follow by gene expression description with all steps – transcription, posttranscriptional splicing and translation. Afterwards, there is an analysis of introns importance, introns evolution theories and similarities among different organisms mentioned, follow by some introns recognition methods. Practical part is focused on the initial and terminal regions of introns and conservative dinucleotide sequences verifying. The thesis studies intron – exon and exon – intron boundaries. The last part tries to suggest new potentially conservative sequences – patterns, search for them and check their conservativeness.
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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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Methods for class prediction with high-dimensional gene expression data
Šilhavá, Jana ; Matula, Petr (referee) ; Železný, Filip (referee) ; Smrž, Pavel (advisor)
Dizertační práce se zabývá predikcí vysokodimenzionálních dat genových expresí. Množství dostupných genomických dat významně vzrostlo v průběhu posledního desetiletí. Kombinování dat genových expresí s dalšími daty nachází uplatnění v mnoha oblastech. Například v klinickém řízení rakoviny (clinical cancer management) může přispět k přesnějšímu určení prognózy nemocí. Hlavní část této dizertační práce je zaměřena na kombinování dat genových expresí a klinických dat. Používáme logistické regresní modely vytvořené prostřednictvím různých regularizačních technik. Generalizované lineární modely umožňují kombinování modelů s různou strukturou dat. V dizertační práci je ukázáno, že kombinování modelu dat genových expresí a klinických dat může vést ke zpřesnění výsledku predikce oproti vytvoření modelu pouze z dat genových expresí nebo klinických dat. Navrhované postupy přitom nejsou výpočetně náročné. Testování je provedeno nejprve se simulovanými datovými sadami v různých nastaveních a následně s~reálnými srovnávacími daty. Také se zde zabýváme určením přídavné hodnoty microarray dat. Dizertační práce obsahuje porovnání příznaků vybraných pomocí klasifikátoru genových expresí na pěti různých sadách dat týkajících se rakoviny prsu. Navrhujeme také postup výběru příznaků, který kombinuje data genových expresí a znalosti z genových ontologií.
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