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Origin of karst conduits and caves in Jizera Formation in Turnov.
Slavík, Martin ; Bruthans, Jiří (advisor) ; Schweigstillová, Jana (referee)
Aim of this study is to characterize the processes responsible for evolution of open conduits and caves in Jizera Formation near Turnov, in particular to distinguish if the main factor acting in enlargements of conduits is dissolution and the conduit system can be called karst, or if the process is caused by erosion of weakly cemented sandstone without contribution of dissolution. An important part of the study is to introduce the concept of self-organization. Based on results from accelerated simulation of dissolution of twenty rock samples, SEM analysis and drilling resistance, I have proved that rocks in Jizera Formation near Turnov dissolve in an acidic environment and their strength characteristics does not enable direct erosion by flowing water. Samples from localities of "Bartošova pec", "Slepé údolí Podhorčí", "Rozsedlinové ponory pod Drábovnou", "Šetřilovsko", "U Kačeny" and "Semikraska" dissolve, but behavior of samples from "Sudoměř - rybník" and "Sudoměř - Skalský potok" is in an acidic environment very similar to samples from Teplice Formation "Skalní pískovcový výchoz u Podhorčí" and "Valdštejn".
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Karstification of carbonato-silicate rocks: review of literature and leaching experiments
Vojtíšek, Jan ; Bruthans, Jiří (advisor) ; Kůrková, Iva (referee)
The process of karstification doesn't occur only in easily soluble rock, such as limestone and evaporites, but also occurs in other rocks such as quartzites or siliciclastic rocks with carbonate cement. The "ghost rock" karstification is, unlike the classical karstification, two- step process, where the soluble component are dissolved first and subsequently the insoluble components are eroded and flushed away. These processes also occur in the Czech Republic, for example in the Bohemian Cretaceous Basin (BCB). Practical part of this thesis consists of leaching experiments of samples from BCB. Leaching in hydrochloric acid is an accelerated simulation of natural processes of dissolution by acidic solutions. Leaching of the samples in acid led to the decrease of sample strength, sometimes to their desintegration. The samples are probabbly prone to the evolution of karst conduits. Leaching experiments showed that the carbonate content is an important but not the only driving factor in the karstification process.
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Detection of genetic modifications associated with pancreatic adenocarcinoma
Urbančoková, Alexandra ; Smolková, Katarína (advisor) ; Alán, Lukáš (referee)
Pancreatic ductal adenocarcinoma (PDAC) is a serious oncological disease, which ranks among cancers with the worst prognosis and a three-year life expectancy of 10%. Ex-vivo organoid cultures derived from cancer tissue are popular and reliable research models, which reflect the morphology and histology of the original tissue. Genetic background leading to development PDAC confer typical alterations in genes KRAS, TP53, SMAD4 a CDKN2A. The aim of this thesis was to determine mutations present in organoid cultures derived from human PDAC. We used online genomic databases to estimate specific mutations typical for PDAC. Based on that research we designed protocols for the detection of PDAC genetic alterations and optimized those methods using cultured cells. We applied the approach on primary ex- vivo organoids derived from surgical cancer specimens and detected mutations in KRAS, TP53, SMAD4, or deletion of exons in CDKN2A. Alternatively, we proposed improvements for the analysis of genetic background in PDAC. The data obtained within this thesis will be used for the stratification of metabolomics and biochemical analyses further in the project.
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Molecular analysis of head and neck carcinomas associated with HPV infection
Glendová, Kristýna ; Staněk, Libor (advisor) ; Tachezy, Ruth (referee)
Head and neck cancers (HNSCC) are highly heterogeneous disease, results from two major carcinogens - tobacco and/or alcohol, or HR HPV infection. This thesis was based on 60 biopsies of head and neck tumours embedded into paraffin after histological verification. HPV infection, including particular types was monitored in different HNSCC regions by multiplex qPCR. Subsequent IHC demonstrated expression of p16INK4A and p53 as a possible diagnostic biomarker. Based on the information, patients with HNSCC can benefit from antiEGFR therapy by Cetuximab, but so far without defined predictors, the analysis of point mutations of Ras gene family (Kras, Nras) and Braf gene was performed. These mutations were monitored as potential predictive biomarkers, in correlation with gender, age and other risk factors. For all statistical processing the Chi-x2 test was used. Key words: Head and neck cancers, biopsy, HPV types, PCR, p16INK4A, p53, molecular predictors, Kras, Nras, Braf
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Possibilities of karstification of calcareous sandstones in the Jizera segment of the Bohemian Cretaceous Basin and evolution of conduits in the thick-bedded sandstones
Vojtíšek, Jan ; Bruthans, Jiří (advisor) ; Vysoká, Helena (referee)
Features typical for karst, such as fast groundwater flow and existence of open conduits were observed in various parts of Bohemian Cretaceous Basin (BCB). So far, vertical and areal extent of karst rocks is not known. In case of concerning conduits in quartz sandstones the observation of their evolution in profiles perpendicular to flow is missing. The thesis deals with above mentioned issues. Concerning potential to karstification it is limited to Jizera facial area of BCB. For this purpose, leaching of samples in hydrochloric acid were carried out. The hydrochloric acid was used as an accelerated simulation of natural processes of dissolution of rock by acidic solutions. The reaction of samples on leaching in acid, disintegration and content of the CaCO3 component were evaluated. CaCO3 content was determined also by calcimetry. Rocks which disintegrated can be a suitable for the evolution of karst conduits. According to the lithostratigraphic sections, the examined profiles belong to the TUR5 and TUR6 units - thus these units contain rocks suitable for the evolution of karst conduits. In Předměřice site about 23 % of samples disintegrated, in Kosmonosy site 8 % and in Turnov site 36 % disintegrated. Thus about 1/10 to 1/3 of tested profiles is prone to karstification and evolution of karst...
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Molecular analysis of head and neck carcinomas associated with HPV infection
Glendová, Kristýna ; Staněk, Libor (advisor) ; Tachezy, Ruth (referee)
Head and neck cancers (HNSCC) are highly heterogeneous disease, results from two major carcinogens - tobacco and/or alcohol, or HR HPV infection. This thesis was based on 60 biopsies of head and neck tumours embedded into paraffin after histological verification. HPV infection, including particular types was monitored in different HNSCC regions by multiplex qPCR. Subsequent IHC demonstrated expression of p16INK4A and p53 as a possible diagnostic biomarker. Based on the information, patients with HNSCC can benefit from antiEGFR therapy by Cetuximab, but so far without defined predictors, the analysis of point mutations of Ras gene family (Kras, Nras) and Braf gene was performed. These mutations were monitored as potential predictive biomarkers, in correlation with gender, age and other risk factors. For all statistical processing the Chi-x2 test was used. Key words: Head and neck cancers, biopsy, HPV types, PCR, p16INK4A, p53, molecular predictors, Kras, Nras, Braf
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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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Tvorba databáze krasových jevů na území ŠLP Křtiny z dat leteckého laserového skenování
Balková, Marie
This diploma thesis deals with description of the karst and its typical phnenomenons with emphasis on surface figures sinkholes. Further, it dicribes the airborne laser scanning (ALS) technology, data collection and processing procedure and utilization for the puropose of terrain depressions indentification based on the researches and processes of foreign experts. From these available studies, the most suitable methodics is chosen and applied to Digital Elevation Model of 5th generation (DEM 5G) data. The results of this aplication are compared with available sinkholes databases kept in the PLA Moravian Karst office and own terrain research.
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Karstification of carbonato-silicate rocks: review of literature and leaching experiments
Vojtíšek, Jan ; Bruthans, Jiří (advisor) ; Kůrková, Iva (referee)
The process of karstification doesn't occur only in easily soluble rock, such as limestone and evaporites, but also occurs in other rocks such as quartzites or siliciclastic rocks with carbonate cement. The "ghost rock" karstification is, unlike the classical karstification, two- step process, where the soluble component are dissolved first and subsequently the insoluble components are eroded and flushed away. These processes also occur in the Czech Republic, for example in the Bohemian Cretaceous Basin (BCB). Practical part of this thesis consists of leaching experiments of samples from BCB. Leaching in hydrochloric acid is an accelerated simulation of natural processes of dissolution by acidic solutions. Leaching of the samples in acid led to the decrease of sample strength, sometimes to their desintegration. The samples are probabbly prone to the evolution of karst conduits. Leaching experiments showed that the carbonate content is an important but not the only driving factor in the karstification process.
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Optimization of miRNA analysis in fine-needle biopsy samples of pancreatic cancer tissue.
Čuperková, Romana ; Benešová, Lucie (advisor) ; Kuthan, Martin (referee)
Pancreatic cancer (PC) is extremely severe malignant disease with a five-year survival of less than 5%. Currently there is no reliable tool for the diagnosis of PC in its early stages. At the time of clinical symptoms most patients are in an advanced stage of the disease and the treatment does not usually have a significant effect. For these reasons emphasis is gradually shifting to the search for the suitable molecular markers for improvement of the diagnosis and assessment of the survival prognosis with respect to a possibility of surgical treatment. MiRNA represent one of the most promising markers, although, their examination in pancreatic tissue is a complicated process. One of the reasons is the very small amount of the source material coming from a fine needle biopsy. A second cause of problems is the subtle character of the pancreatic tissue resulting in significantly lower yields of molecular genetic analysis when compared to other epithelial tissues. An additional negative factor is heterogeneity of the tissue resulting in disproportionate representation of tumor cells within the sample. A suitable choice of procedures for isolation of nucleic acids (NA) and subsequent analysis including quantification of tumor cells is critical for accurate evaluation of the miRNA levels. This work is...
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