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Gene regulation in Clostridium beijerinckii NRRL B-598
Schwarzerová, Jana ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
Diplomová práce se zabývá studiem genové regulace v Clostridium beijerinckii NRRL B-598, pro následné odvození genové regulační sítě bakterie C. beijerinckii NRRL B-598. V teoretické části této práce je uvedena obecná nomenklatura problematiky genové regulace se zaměřením na nomenklaturu genových regulačních sítí. Následně jsou zde popsané laboratorní metody, sloužící pro získání vhodných dat popisující expresi genů. Tato data jsou základem pro studium genové regulace a návrhy genových regulačních sítí. Práce se zaměřuje především na technologii RNA-Seq a stručný popis laboratorních dat získaných ze zmíněné bakterie C. beijerinckii NRRL B-598. V praktické části se práce zabývá předzpracováním těchto surových laboratorních dat a následným studiem genové regulace se zaměřením na odvození operonů a vytvoření prvních genových regulačních sítí pomocí různých přístupů pro C. beijerinckii NRRL B-598.
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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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Comparison and characterization of salivary proteins from Sergentomyia and Phlebotomus sand flies
Polanská, Nikola
Sand flies (Diptera, Phlebotominae) are small biting insects and vectors of Leishmania spp. which cause medically and veterinary important disease - leishmaniasis. During the piercing of the host skin, sand fly females inject saliva to facilitate the blood feeding. The sand fly saliva is composed of many bioactive molecules which were shown to possess anti-inflammatory and anti-haemostatic functions. The saliva affects host's immunity in the bite site and consequently enhances the survival and development of transmitted pathogens. Most of the studies focus on salivary proteins and enzymes of sand flies belonging to Phlebotomus and Lutzomyia genera, while salivary proteins from sand flies of the third genus Sergentomyia were neglected so far. In this thesis we focused on comparison of salivary proteins from two Phlebotomus species, namely Phlebotomus perniciosus and Phlebotomus orientalis, and Sergentomyia schwetzi. These sand fly species differ not only by the ecology and geographical distribution but also by host preferences. Both Phlebotomus species prefer large or medium-size mammals as the bloodmeal source, particularly rabbits, hares and dogs for P. perniciosus and cattle, goats, sheep and humans for P. orientalis. Contrarily, Sergentomyia sand flies are known for preferred feeding on reptiles...
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Effects of peripheral inflammation on gene expression modulation in passerines and parrots
Kuttiyarthu Veetil, Nithya ; Vinkler, Michal (advisor) ; Hyršl, Pavel (referee) ; Harazim, Markéta (referee)
(English) Birds have well-defined roles in maintaining the ecological balance as predators, seed dispersers, nutrient cyclers, and pollinators making them an integral part of many ecosystems. Birds are often the flag-ship species and are important for wildlife preservation. Some of the avian populations are very well connected across the globe through their annual migration, increasing risks of epidemics of infections. Birds also face different levels of existence encounters in challenging living conditions like deserts and cold mountains. To cope with these diverse environments not only need physiological adaptations, but also a very well-equipped immune system, optimised to challenges common to the environment they inhabit. How well a host immune system responds to pathogens determines the overall fitness of the organism and its survival. Insight into the avian immune system functions is of great significance as birds are reservoirs of innumerable pathogens. They have been the primary source of several major epidemics' onset leading to worldwide human and animal fatalities (e.g., COVID-19, Avian influenza, or West Nile virus outbreaks). Similar to all living beings, avian hosts and pathogens are always in a continuous adaptational arms race. This coevolution of hosts and their pathogens forms the...
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Bioinformatic analysis of RNA dynamics during mammalian oocyte-to-embryo transition
Horvat, Filip ; Svoboda, Petr (advisor) ; Bruce, Alexander (referee) ; Vioristo, Sanna (referee)
The oocyte-to-embryo transition (OET) is a complex biological process during which a terminally differentiated oocyte undergoes numerous and coordinated changes to emerge as a collection of totipotent cells - initial blastomeres of a preimplantation embryo. In mammals, this process is primarily controlled through post-transcriptional regulation of maternal RNAs and transcriptional induction of zygotic RNAs. Technological advancements of next-generation sequencing methods during the last decade enabled studying OET through bioinformatic studies of high-throughput transcriptomics and genomics datasets. The work presented in this thesis explores mechanisms of post-transcriptional regulation and dynamics of different RNAs during OET by utilizing in-depth computational analyses. The presented work is divided into three topics, all covering distinct regulatory facets of the mammalian OET and illustrating roles of different RNA species. The first topic discusses dynamics of maternal transcriptomes in mouse. In our research, we explored roles of deadenylase CNOT6L in the maternal mRNA turnover in mice. We provided evidence that animals deficient in Cnot6l expression are subfertile, due to disruption in deadenylation and degradation of maternal mRNAs deposited in the oocyte. In another study, we...
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Gene expression analysis on a subgene level
Kloda, František ; Fišer, Karel (advisor) ; Novotný, Marian (referee)
RNA sequencing allows investigation of expression of singular genes in cells. It is possible to interpret the arisen data on multiple levels, each level providing a different type of information. Apart from measuring expression of whole genes, it is possible to quantify expression of singular exons, or transcripts (gene isoforms), which allows more detailed study of regulatory mechanisms. The main difference between approaches is in determining the origin of short reads. This step is significantly more complex in analysis of expression of transcripts, as transcripts derived from the same gene have typically larger rate of sequential similarity. In this thesis, we describe eleven tools for subgene level expression analysis a as comparison we have tested three of these tools on real patient data. The results provided by all three tools proved to be very similar with the greatest difference being the time needed for the analysis.
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Transcriptional changes associated with melanoma resistance to small inhibitor treatment
Dorčáková, Terézia ; Kolář, Michal (advisor) ; Modrák, Martin (referee)
Malignant melanoma is an aggressive skin tumour with increasing incidence and, in advanced stages, limited therapeutic results. The major oncogenic alteration in melanoma is mutational activation of the B-Raf protein, with the predominant mutation V600E, which occurs in 60% of cases and hyperactivates the ERK signaling pathway. This cascade of Raf, MEK and ERK protein kinases is an integral part of an evolu- tionarily conserved signaling network that allows eukaryotic cells to sense a variety of extracellular signals. These protein kinases sequentially activate each other and translate extracellular signals into cellular responses such as proliferation, di↵erentiation, cell cycle changes, apoptosis or cell migration. The central role of the ERK pathway in oncogen- esis has made it one of the targets for therapeutic intervention, and inhibitors targeting mutant Raf, such as vemurafenib or dabrafenib, have been approved for the treatment of melanoma. These molecules specifically target B-Raf(V600E) and have led to a revo- lution in melanoma treatment. Unfortunately, such targeted therapy is complicated by the ability of cancer cells to acquire resistance. The aim of this work is to study at the transcriptional level the emergence of this resistance in patients who respond well to treatment and in...
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Single-cell RNA sequencing in leukemia
Brodská, Johana ; Froňková, Eva (advisor) ; Obr, Adam (referee)
Leukemia is a cancer of hematopoietic cells affecting the whole organism. Currently, there are many treatment options for all disease types, but it is still not always possible to fully cure the patient. The single-cell RNA sequencing method offers a new insight into the heterogeneity of both cancerous and non-cancerous cells in the leukemic environment. This thesis aims to briefly present the method and its history and to highlight current findings about leukemia obtained with the help of it. Keywords leukemia (AML, CML, ALL, CLL), sequencing, scRNA-seq, cells, transcriptome, treatment Okomentoval(a): [o1]: To the reader se v odborné literatuře moc nepoužívá
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Transcriptomic analysis of Mesocestoides corti
Korená, Lucie ; Leontovyč, Roman (advisor) ; Převorovský, Martin (referee)
Some species of parasites, including helminths, can inhibit carcinogenesis in their hosts. The antitumoral effect has been discovered in the tapeworms Taenia crassiceps and Echinococcus granulosus, which genes associated with cancer regression have been identified. The effect of melanoma suppression has also been observed in tapeworm Mesocestoides corti by the Laboratory of Helminthology, Department of Parasitology, Faculty of Science, Charles University, however the mechanism-of-action, remains unknown. For the upcoming research it was essential to have the complex molecular data such as transcriptome of the developmental stage s of M. corti. This work is focused on the transcriptomic profiling of the tapeworm M. corti and the differential gene expression in two different strains of murine hosts (inbred and outbred) using the RNA-Seq. The main goal was to identify upregulated transcripts in the tapeworms from the murine hosts that could have a potential effect on cancer regression. Differential gene expression analysis was performed, and the results showed that tapeworms in murine hosts (regardless of strain) had more upregulated transcripts than tapeworms cultured in vitro. Analysis of highly upregulated transcripts in the tapeworms that were grown in the murine hosts identified several...
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