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Fluorescent Methods in Research of Eukaryotic Cells
Chmelíková, Larisa ; Babula, Petr (referee) ; Pešl,, Martin (referee) ; Provazník, Ivo (advisor)
Tato práce zkoumá aplikaci fluorescenčních metod používaných v in vitro studiích v oblasti regenerace srdeční tkáně. Konfokální fluorescenční mikroskopie je vhodnou mikroskopickou technikou pro výzkum v této oblasti, protože umožňuje vizualizaci 3D struktur a distribuce buněk ve 3D modelech. Používané fluorescenční markery by měly být dlouhodobě stabilní, biokompatibilní a netoxické pro živé buňky. V současné době je použití nanočástic jako superparamagnetické nanočástice oxidu železa (SPION) velmi populární; velké množství studií ukazuje, že jsou vhodné pro dlouhodobé experimenty. Tento výzkum využívá superparamagnetické maghemitové nanočástice svázaným rhodaminem na jejich povrchu (SAMN-R) a popisuje jejích excitační a emisní spektrum, velikost a lokalizaci vbuňkách. Stanovení toxicity bylo provedeno měřením reaktivních forem kyslíku (ROS) a nekvantitativním měřením pomocí fluorescenční mikroskopie bylo zjištěno, že hodnota dávky 20 µg·cm-2 je optimální pro aplikaci na živé buňky. Dále byl zkoumán vliv aplikace SAMN-R na buněčnou proliferaci a motilitu, kdy ve studii buněčné proliferace a scratch assay byla použita buněčná linie fibroblastů 3T3. Poté byla studována migrace jednotlivých buněk s použitím mezenchymálních kmenových buněk (MSCs), izolovaných zlidské tukové tkáně. Následná statistická analýza nepotvrdila, že by aplikace SAMN-R měla významný vliv na buněčnou proliferaci, kolektivní migraci nebo na migraci jednotlivých buněk. Lze tedy předpokládat, že SAMN-R jsou vhodným fluorescenčním markerem pro výzkum živých buněk, včetně experimentů voblasti regenerace tkáně. MSC buňky izolované z tukové tkáně mají velký potenciál v regeneraci srdeční tkáně. Jejich interakce s buněčnou linií srdečních svalových buněk HL-1 byly studovány pomocí scratch assay, kdy se tento model jeví jako nadějný a vhodný pro studium buněčných kontaktů a jejich roli přiregeneraci buněk.
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Electrophoretic and immunofluorescence methods for study of plant cell cultures
Klimešová, Marie ; Babula, Petr (referee) ; Provazník, Ivo (advisor)
In all organisms are rising a reactive oxygen and nitrogen species by the effects of various stress factors and these species have a negative impact on the organism. Due to this species plants have built up an efficient antioxidant system, that helps them to resist negative effects of reactive oxygen and nitrogen species. In this work was researched the effect of hydrogen peroxide and sodium benzoate on the production of hydrogen peroxide, superoxide, reactive nitrogen species and malondialdehyde, contained in the root and above-ground part of maize (Zea mays L.). By use of the fluorescence microscopy there were obtained images of cross-cut of root from which was determined the intensity of fluorescence of individual parts of the root and was examined the effect of the intensity of fluorescence markers of oxidative stress in dependence on the type of the fluorescence filter used.
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Bipartite graphs for microbiome analysis
Šafárová, Marcela ; Provazník, Ivo (referee) ; Sedlář, Karel (advisor)
Microorganisms are all around us. Some of them even live in our body and are essential for our healthy being. Study of microbial communities based on their genetic content has become very popular with the development of new technologies, which enable easy reading of DNA or RNA. The key role of these studies is usually to characterize significant microbial patterns of an environment. However, currently used visualization tools have many drawbacks for such analyses. The subject of this thesis is to design a R/Bioconductor package for simple creation of bipartite graphs from microbial data. This type of visualization brings many advantages for microbiome analysis. Benefits of bipartite graphs are further demonstrated by analysis of main parameters affecting computer processing of microbial data.
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Statistic evaluation of phylogeny of biological sequences
Vadják, Šimon ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The master's thesis provides a comprehensive overview of resampling methods for testing the correctness topology of the phylogenetic trees which estimate the process of phylogeny on the bases of biological sequences similarity. We focused on the possibility of errors creation in this estimate and the possibility of their removal and detection. These methods were implemented in Matlab for Bootstrapping, jackknifing, OTU jackknifing and PTP test (Permutation tail probability). The work aims to test their applicability to various biological sequences and also to assess the impact of the choice of input analysis parameters on the results of these statistical tests.
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PowerCube spirometry measurement
Krajčovič, Martin ; Závodná, Eva (referee) ; Provazník, Ivo (advisor)
This paper is dedicated to the issue of respiratory physiology, human body energy exchange and calorimetry. It describes functions of the PowerCube-Ergo-Device (Ganshorn Medizin Electronic, Germany), which serves ergospirometry measurement and designes a protocol used to measure and evaluate the cardiopulmonary response of the organism and the metabolic activity of the organism in a group of athletes and non-sportspeople. Furthermore, it constitutes an application developed in MATLAB programming environment, allowing graphical portrayal and evaluation of measured data. The final part of this thesis is devoted to statistical evaluation of the data gathered within the selected group of patients.
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ECG Signal Transmission via Ethernet
Bayerová, Zuzana ; Provazník, Ivo (referee) ; Sekora, Jiří (advisor)
The semestral thesis describes ECG signal compression methods designed to modify the data for transmission via communication channels. The thesis contains an introduction to Ethernet and explanation of communication in the network. The transport protocols TCP and UDP are discussed in more detail. In the practical part of the thesis was created two separate applications. The first application in the sender's computer opens a text file with the ECG signal. Loaded ECG signal is filtered by cascade of filters to eliminate interference. The resulting signal is displayed. A part of the application is the R wave detection, calculating the length of RR interval and heart rate. The application also allows to compress an ECG signal. ECG signal is sent via Ethernet network via UDP protocol for individual samples. Applications in the recipient's computer receives signal samples from the network. Recieved compressed data is reconstructed. The resulting ECG signal is displayed and there are again detected R waves, the length of RR intervals and sampling frequency are calculated.
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ECG Wave Delineation
Trnová, Kateřina ; Provazník, Ivo (referee) ; Kozumplík, Jiří (advisor)
This thesis deals with the detailed measurement of one cycle of the ECG signal. data samples of the beginning and end of major sections of this cycle are obtained from the values referred to in the database TESTRO. There is found a representative cycle. The text describes basic types of measuremend intervals, principles of multiple methods of measurement and description of the implemented program. Algorithm for measurement of functional units of ECG cycle signal, which was designed, is based on the detection of trend growth, of the field of signal using the first difference. Functionality was tested on a standard CSE database.
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Comparison of advanced analysis of fMRI data from oddball experiment
Fajkus, Jiří ; Jan, Jiří (referee) ; Provazník, Ivo (advisor)
This master´s thesis deals with processing and analysis of data, acquired from experimental examination performed with functional magnetic resonance imaging technique. It is an oddball type experimental task and its goal is an examination of cognitive functions of the subject. The principles of functional magnetic resonance imaging, possibilities of experimental design, processing of acquired data, modeling of a response of organism and statistical analysis are described in this work. Furthermore, particular parts of preprocessing and analysis are carried out using real data set from experiment. The main goal of this work is suggestion and realization of model, which enables advanced categorization of stimuli, considering the type of previous rare stimulus and the number of frequent stimuli within them. With its in-depth categorization, this model enables detail exploration of cerebral processes, associated mainly with attention, memory, expectancy or cognitive closure. The second point of that work is an evaluation of models of hemodynamic response, which are applied in statistical analysis of data from fMRI experiment. Comparison of basis functions, the models of hemodynamic response to experimental stimulation used for general linear model, is performed in this work. The result of this comparison is an evaluation of detection efficiency of activated voxels, false positivity rate and computational and user difficulty.
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Adaptive Digital Filtering of Biological Signals
Ištok, Martin ; Kozumplík, Jiří (referee) ; Provazník, Ivo (advisor)
The main objective of this bachelor’s thesis was to describe adaptive digital filtering theory including different types of the adaptive algorithm and adaptive filter. An adaptive systém is used for power line interference canceller for ECG signal. The thesis includes design of 4 adaptive filters: simple adaptive filter, simple adaptive notch filter, adaptive notch filter using resonator and adaptive notch filter using adaptive resonator. It also contains basic testing of the filters based on different settings. Different settings are also evaluated.
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Homologous Gene Finding
Lýčková, Veronika ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This diploma thesis deals with the description of homologous genes and molecular biological databases that are used for their search and allow comparison. Among the most important institutions that deal with data management and analysis, include the EBI, NCBI and CIB. For searching homologous genes is the most fundamental NCBI - National Center for Biotechnology Information. More attention is paid to the search algorithms of homologous genes such as BLASTN and PatternHunter. The practical part of this thesis is the implementation of the algorithm comparing two sequences and locating homologous genes. The comparison is made on the basis of the nucleotide sequence and amino acid sequence. The results generated from the program will be further compared with results from commercially available programs.
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