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Morphogenesis of the bacterial colonies and their mutually influencing
Rieger, Tomáš ; Markoš, Anton (advisor) ; Rulík, Martin (referee) ; Kuthan, Martin (referee)
This thesis follows previous works of our group (Rieger T. et al., 2008; Cepl J. et al., 2010 and Patkova I. et al., 2012), where we focused on the morphology of the bacterial colonies Serratia marcescens and its variety caused by changing of the inoculation conditions on nutrient agar. When bacterial colonies S. marcescens are grown on nutrient agar enriched with glucose isolated enough from other colonies in its living space, it can form coloured structured colonies, which we named morphotype "fountain" (F). This morpotype becomes ideal for following studies of mutual influencing of the bacterial colonies, because of its ability of pigmentation change or structure loss caused by altering surrounding inoculation conditions. We noticed in normal sowed agar plates, that bacterial colonies, which grows in the close distance with other colonies develop their pigmentation sooner, than colonies, that grows more isolated. We studied how is this influencing happening and what are the necessary conditions for it. We proved, that different species of bacterial macrocolonies (S. marcescens - morphotype (M), S. rubidea and E. coli) emits into the nutrient agar informative signal, which makes the recipient colonies S. marcescens reacts on this signal with the same manner (X structure). It looks, that this is...
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Yeast colonies as a model of multicellular behaviour of microorganisms
Kuthan, Martin ; Palková, Zdena (advisor) ; Hašek, Jiří (referee) ; Kolarov, Jordan (referee)
- 32 - Závěr Již v úvodu jsem se zmínil, že mnohé laboratorní kmeny kvasinek ztratili vlivem domestikace schopnost filamentálního růstu. Ukázkovým příkladem cílené domestikace je laboratorní kmen S288C. Historie vzniku tohoto kmene je zajímavá a dokumentuje výrazný vliv genetiků na jeho vlastnosti. Velké množství kmenů S. cerevisiae používaných v laboratořích má společného předka kterým je kmen EM93. Tento diploidní kmen izoloval v Kalifornii v roce 1938 Emil Mrak z hnijícího fíku (MORTIMER and JOHNSTON 1986). Není však jasné, zda se jednalo o přirozenou mikroflóru fíků, nebo o kontaminaci komerčními pekařskými či kvasnými kmeny. Kmen EM93 je heterothalický a je schopen filamentálního růstu (LIU et al. 1996). Pro laboratorní účely ale nebyl úplně ʺpohodlnýʺ. Protože tvorba shluků buněk brání izolaci klonů vzniklých z jediné buňky a ztěžuje přesné určení počtu buněk v tekutých kulturách, snažili se genetici získat prototrofní kmen s neadherujícími, dobře resuspendovatelnými buňkami. Mnohonásobným křížením haploidních segregantů kmene EM93 s dalšími laboratorními kmeny a komerčními pekařskými kmeny vytvořil Robert Mortimer kmen S288C, jehož 90 % genomu pochází...
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Development and validation of a new method for enrichment and detection of circulating tumor DNA in cancer patients
Pláničková, Lenka ; Minárik, Marek (advisor) ; Kuthan, Martin (referee)
Tumors are one of the leading causes of death worldwide. Generally, the prognosis is better if the treatment begins at an early stage. Nowadays, the conventional chemotherapy treatment of cancer, known for its limited efficacy and side effects, is being gradually replaced by targeted biological treatment, which is used when specific genetic mutations are found. A part of the treatment is a detection of a potential progression, which is mainly based on the tumor biomarkers monitoring. Currently, further investigation of a so-called liquid biopsy method are ongoing, on which this thesis is focused. The main aim of this work was the experimental development and validation of the method for detection of the ctDNA in the plasma samples based on the somatic mutations presence. For the development and optimization of the system on the principle of denaturation capillary electrophoresis, the samples of cancer patients with KRAS mutation were used. Subsequently, a clinical part of the research was performed on a pilot set of 21 plasma samples. Finally, the method was optimized for the detection of BRAF and EGFR markers. A partial objective was to improve the detection sensitivity and increase the capture of the ctDNA in patients with advanced stage of the disease. The results of this work suggest the...
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Intrinsic transcription termination by multisubunit RNA polymerases
Vojáčková, Jitka ; Sýkora, Michal (advisor) ; Kuthan, Martin (referee)
Transcription is a process of genetic information rewriting from DNA sequence to RNA copy by DNA dependent RNA polymerase. Two mechanisms of transcription termination are known for bacteria: intrinsic transcription termination, independent of any accessory factors, and transcription termination dependent on proten factor called Rho. Intrinsic transcription termination is common mainly for bacteria, yet different, but partially similar forms of intrinsic transcription termination occur also in eukaryotes and archaea. This thesis includes a brief summary of RNA polymerase structure and elongation complex stability, describes individual steps of intrinsic transcription termination mechanism in bacteria including all disscused models and gives examples of intrinsic transcription termination in eukaryotes and archaea and their comparison with bacterial model of intrinsic transcription termination. Key words: RNA polymerase, elongation complex, intrinsic transcription termination, hairpin RNA structures
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