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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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The role of the immune system in colorectal and ovarian cancer
Kocián, Petr ; Hoch, Jiří (advisor) ; Prausová, Jana (referee) ; Žaloudík, Jan (referee)
Prediction of clinical outcome in cancer is usually achieved by histopathological evaluation of tissue samples obtained during surgical resection of the primary tumor. Traditional tumor staging (AJCC/UICC-TNM classification) summarizes data on tumor burden (T), presence of cancer cells in draining and regional lymph nodes (N) and evidence for metastases (M). However, it is now recognized that clinical outcome cansignificantly vary among patients within the same stage. Data collected from largecohorts of human cancers has demonstrated the impact of immune-classification, which has a prognostic value that may add largely to the significance of the AJCC/UICC TNM-classification. In our study we examined the immune cells that infiltrated the tumor tissues of colorectal and ovarian cancer patients. In a cohort of newly diagnosed colorectal cancer patients we examined the correlations between the KRAS mutational status, patterns of tumor-infiltrating immune cells and the presence of tumor recurrence. Our data suggest that colorectal cancer patients with low levels of tumor-infiltrating lymphocytes, a high CD1a/DC-LAMP tumor-infiltrating dendritic cells ratio, and a KRAS mutation in codon 13 are at a high risk of disease recurrence. In ovarian cancer patients we focused on the dynamics of the tumor-infiltrating...
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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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Hydrology of Amateur cave and sinking streams focused on tracer tests
Gregorová, Anita ; Bruthans, Jiří (advisor) ; Vojtěchová, Anna (referee)
This study briefly summarizes methodology of tracer studies in karst areas (the way how they were carried out and their evaluation). Second part of the study specifies geological, hydrogeological and hydrological situation of the area of interest - northern part of the Moravian Karst, surroundings of Sloup - using available literature on that topic. Description of the area was completed with field measurements done by the author. Their results can be used as a basis for possible future surveys.
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Possibilities of Karstification in the Transitional Facies of the Bohemian Cretatious Basin
Balák, František ; Bruthans, Jiří (advisor) ; Knížek, Martin (referee)
In the region of Bohemian Cretaceous Basin can be found some springs with specific yield over 100 l/s. The doyen of Czech hydrogeology Prof. Hynie described some of those springs to be of karst origin and as the most permeable area he described the so-called transitional facies between shallow-water sandstones and deep-water marlstones. Possibilities of karstification have not yet been studied for rocks in the BCB, so the origin of well-permeable pathways in the BCB is a subject of speculations. This thesis deals with the question of which sedimentary rocks potentially allow the generation of karst permeability in the BCB. To do so, rock samples drilled from outcrops in the BCB were subjected to a fast dissolution simulation by leaching in hydrochloric acid. Carbonate content is measured by a standard and one's own method. Mineral composition, grain size and microscopic structure of rocks are studied with SEM. As is shown, the border of rock karstification is not defined just by the carbonate content, but also the grain size, rock structure and by the occurrence of fine secondary silicate content. Concerning the amount of dissolvable compounds, the border of total disintegration can be at 30 % of carbonate content for some rocks, but the most resistant rocks (mostly fine rocks with SiO2 matrix) stay intact...
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Caves and their legal protection
Chvátalová, Eva ; Damohorský, Milan (advisor) ; Sobotka, Michal (referee)
This diploma thesis aims at Czech legislation related to conservation of caves both in terms of its link to the protection of caves as subterranean spaces and parts of the natural environment and of its relation to other fields of expertise, including legal studies (e.g., mining law) and other disciplines (e.g., geology, carsology). First, our attention is paid to definition of the term "cave" and to links of the term to natural sciences. Further, we analyse the development of legal conservation of caves and approaches to caves as a subject of legislation per se. The example of Slovenia - being a prominent speleological country with recognized legislation in terms of its quality and detail - is used in order to compare Czech approaches to cave conservation. Concerning the practical issues, we present an example of conservation effort devoted to one single cave in Czechia, which enables to describe functioning of legal conservation tools, including the themes where these tools overlap. We also present and discuss the only one Czech case-law dealing with the legal aspect of caves.
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Effects of Municipal Wastewater Treatment Plant at Lopac Sinkhole Cave System
Ondruš, Martin ; Gruberová, Eva (referee) ; Malá, Jitka (advisor)
The aim of this thesis is to assess the impact of water outflow from wastewater treatment plant on karst rivers. The study was done in the northern area of Moravský kras protected landscape, where the impact of WWTP Ostrov u Macochy on a cave system Lopačské propadání was studied. As a part of this study a half-year monitoring was carried out, which consisted of water sampling every two weeks. In total, 13 water samples were taken from 7 sampling points. Moreover, flow rate, temperature, conductivity, oxygen concentration and pH were measured at the sampling point. Afterwards, the content of undissolved solids, COD, BOD, N-NH4+, N-NO2-, N-NO3-, NKi and total phosphorus were determined in the samples. The change of parameters in time on the sampling points and further along the flow of the river was evaluated from the measured values. The outflow values from waste water treatment plants were compared with the emission limits for surface waters and the values of river water parameters were compared with the environmental quality standards. It wasn’t proven that the outflow from the observed waste water treatment plant is negatively influencing the water stream. The most serious problems are: -The WWTP was designed for treatment of sewage from Ostrov u Macochy, which involved separate sanitary and storm sewers. After finishing the WWTP, a uniform sewer was built. -High concentration of total phosphorus on the outflow from WWTP. -Poor quality of Lopač brook water already before the outflow vent from WWTP.
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Effect of effluent from wastewater treatment plants on karst rivers
Schrimpelová, Kateřina ; Gruberová, Eva (referee) ; Malá, Jitka (advisor)
Karst rivers are special type of rivers because of their hydrography conditions. They usually flow from non-karst area and as soon as they reach in to the karst area they disappear underground. There, they flow through cavities until they reach the surface again. The aim of this thesis is to assess the impact of water outflow from wastewater treatment plant on karst rivers. The study was done in the central area of CHKO Moravský kras where the impact of two WWTP on a cave system Rudické propadání – Býčí skála is evaluated. As a part of this study a half-year monitoring was carried out, which consisted of water sampling once every two weeks. In total, 13 water samples were taken from 8 sampling points. Also 4 additional one-time samples were taken from the cave system. Moreover, flow rate, temperature, conductivity, oxygen concentration and pH were measured at the sampling point. Afterwards, the content of undissolved solids, CODCr, BOD, N-NH4+, N-NO2-, N-NO3-, P-PO43- and total phosphorus were determined in the samples. The change of parameters in time and during the flow in the river was observed from the measured values. The balance of pollutants in particular parts of the river was calculated. The outflow values from waste water treatment plants were compared to the emission limits for surface waters and the parameters of rivers were compared to the environmental quality standards. According to the results, it can be observed that the water quality improves after passing through the cavities. It was proven that the outflows from the observed waste water treatment plants are negatively influencing the water streams. The most serious problem is the wash up of sludge from WWTP Rudice and its consequent sedimentation in the river and/or outflow to the Rudické propadání.
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Map of the Dratenická Cave Surroundings in Moravian Karst
Hanuš, Vojtěch ; Švábenský, Otakar (referee) ; Weigel, Josef (advisor)
The aims of my diploma thesis are the design of a map of Drátenická cave surroundings in the Moravian Karst in the 1:500 scale with details utilizable by speleologists and the examination of a map of 1945 depicting the region of Drátenická cave. The thesis includes an elaboration of the theoretical foundations relevant for the fulfillment of the aims and the descriptions of the geodetic and processing procedures. The outcome of the thesis is the planimetric and altimetric survey, a new digital map of the region and the final examination of planimetric and altimetric components of the map of 1945.
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