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A comparison of metabarcoding and morphology-based identification of protist communities
Tučková, Kateřina ; Škaloud, Pavel (advisor) ; Steinová, Jana (referee)
This thesis is focusing on metabarcoding; its history, principles and current use in science. Metabarcoding brings us a new way to observe a diversity of protists. Although the protists are ubiquitous on the Earth and play a key role in the majority of biological processes, our knowledge of their diversity is still very poor. Traditional microscopy techniques are mostly based on morphology-based identification of taxa. However, they are not so suitable for investigating protist diversity due to their small size, low concentration in the environment, and the convergent morphological evolution of many groups. Similarly, the metabarcoding has its pros and cons, as well. This thesis summarizes pros and cons of both techniques, trying to emphasize the need to both of them to gain a more complete insight into the diversity of protists on the Earth.
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Hematopoiesis in the models of zebrafish and medaka as a recipient for human HSC xenograft
Pravcová, Naďa ; Drbal, Karel (advisor) ; Svoboda, Ondřej (referee)
Danio rerio (zebrafish) and Oryzias latipes (medaka) have recently become popular model organisms to study hematopoiesis. These model organisms present several advantages in comparison to other commonly used models, the most common being Mus musculus (mouse). The advantages are shorter generation time, large offspring production, frequent spawning, external fertilization and development, the optical transparency of embryos amenable to genetic manipulation on the background of vast numbers of transgenic lines (mainly in zebrafish) and inbred strains (in medaka). Moreover, most of the mechanisms behind zebrafish and medaka hematopoiesis are conserved in higher vertebrates. Most importantly, the optical transparency in early development and in adult mutant transparent strains allows for observation of hematopoietic stem cell (HSC) development in vivo. Therefore, it is possible to generate humanized fish using xenotransplanted human HSCs for studies of the engraftment, differentiation, and trafficking of human HSC in vivo. Currently, the most popular organism for human HSC xenotransplantation is mice. This model system is not suitable for in vivo imaging of HSC engraftment. Moreover, a prior immunodepletion step is necessary. The process of immunodepletion includes genetic manipulation or irradiation...
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Bioinformatical analysis of the complex multidimensional microscopy datasets
Backová, Lenka ; Černý, Jan (advisor) ; Čapek, Martin (referee)
Microscopy is embedded in the history of life sciences and vice versa. Recent advances in the field present new challenges as new revolutionary technologies arise. Sample prepa- ration, microscope operation and data analysis have become particularly demanding re- quiring specific interdisciplinary expertise. Bioimaging data analysis is computationally demanding, as microscopy technologies can easily acquire data of exceptional size, often in terabytes. Correct analysis requires computer vision knowledge, as well as knowledge of studied biological systems and last, but not least deep understanding of microscopy technology. Tools available for the analysis of the imaging data vary from open-source customizable software with a coverage of multiple tasks to a task specific proprietary software. To choose the best tools for the analysis, analysts should know their options and tasks at hand. In bioimage analysis the tasks needed to be employed depend on the desired outcome and the acquisition technology. Amongst the possible tasks to con- sider belong deconvolution, segmentation and registration. Amount of approaches and algorithms available is progressively growing, resulting in a complex field, difficult to be easily familiar with. My thesis covers different microscopy technologies with emphasis on...
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Investigation of deformation mechanisms in Mg-Gd alloys
Szabóová, Andrea ; Mathis, Kristián (advisor) ; Drozdenko, Daria (referee)
Title: Investigation of deformation mechanisms in Mg-Gd alloys Author: Andrea Szabóová Department: Department of Physics of Materials Supervisor: doc. RNDr. Kristián Mathis, DrSc. Abstract: In the present work, the deformation behavior of magnesium-gadolinium binary alloys was investigated. Dependence on the concentration of Gd and deformation temperatures was studied. Extruded samples had relatively strong initial texture. Compression tests were done at room temperature and 200řC. Simultaneously with deformation acoustic emission was recorded. Data from acoustic emission was analyzed with advanced statistical methods. Results of the combination of these two experimental methods indicated that at the beginning of the deformation twinning is the dominant mechanism. In the following stage of plastic deformation non-basal slip systems became the governing deformation mechanism. With higher content of Gd the size of twins decreases as a result of the decreased mobility of twin boundaries caused by solute atoms. At higher temperatures twinning activity was increasing. In addition, results were confirmed by optical light and scanning electron microscopy. Keywords: magnesium alloy, deformation tests, acoustic emission, microscopy
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Evaluation of upper secondary students' microscopy skills
Míková, Zuzana ; Janštová, Vanda (advisor) ; Mourek, Jan (referee)
High-school students are less interested in science then before. Despite importance of science for our life and for description of nature around us, students lose motivation for studying it. The approach of teacher is critical for focusing students' attention. Lessons should be based on linking of the education with daily-life and biology provides plenty of possibilities to achieve the goal, especially employing hand-on education, practical examples and exercises. One of the most effective way to show the beauty and a complexity of organism structure is by using microscopes. Many different techniques have been used to prepare education materials - picture, videos or whole movies from micro-word. Nevertheless, a classical optical microscopy is by far the most common training activity during the practical courses. An evaluation of this education aspects is, therefore, critical for further method development. This diploma thesis is focused on establishing of evaluation techniques and subsequent analysis of the current state of students' microscopy skills. First of all, the elementary set of knowledge and the correct microscopy work-flow were established in collaboration with eleven experienced teachers. Based on these results, two types of surveys were designed. One of them was dedicated to teachers...
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Luminescence Diagnostic of Photovoltaic Cells
Stojan, Radek ; Frantík, Ondřej (referee) ; Šály,, Vladimír (referee) ; Vaněk, Jiří (advisor)
Diagnostic of photovoltaic cells defects is one of the key step in production. This dissertation thesis deals about diagnosis of photovoltaic cells by radiative recombination of electron - hole pairs. This radiative recombination is known as luminescence. Diagnostic methods using this local light emission in infrared region have innovative potential. The method of electroluminescence is one of the most widely used luminescence methods whose modifications are applied across the industry, especially in semiconductors. The main area of this thesis research is focused on non-destructive analysis of radiated infrared radiation of monocrystalline and polycrystalline solar cells in various modifications of standard electroluminescence method. In this research there are used two types of CCD cameras are used as luminescent radiation detectors. Method of photon emission microscopy is used for magnification element. Local light emission inspection by microscopy should have benefit to qualitative evaluation of solar cells defects. Radiation emitted by the solar cell has a wave character. This fact brings the potential of using some of the characteristics of the waves. We are talking about the intensity and mainly about new characterization by polarization during the detection of defects in the solar cell surface. Innovation of the measuring workplace of the standard electroluminescence method to use polarization analysis is one of the goals of this dissertation thesis.
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Leucocytozoon and methods of its detection in raptors
Sekerášová, Iveta ; Brzoňová, Jana (advisor) ; Majerová, Karolina (referee)
The genus Leucocytozoon is a bird parasite. Its hosts constitute usually of representatives of the Falconiformes group and hawks (Accipitridae). The vector of this parasite are blackflies (family Simuliidae). This thesis brings an overview of species of the genus Leucocytozoon so far detected in birds of prey. The thesis focuses primarily on methods of detecting Leucocytozoon in hosts. Traditionally, this genus has been described on the basis of its morphological characters observed via microscope. With the discovery of polymerase chain reaction method (PCR), the detection possibilities expanded and allow us to study this parasite on molecular levels. The thesis contains a basic overview of detection methods, characteristics of their principles and outlines their strengths and weaknesses regarding the practical applicability as well. Based on that, the microscopic approach alongside with the detection based on molecular methods is recommended.
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Native hyaluronan as a delivery system for hydrophobic drugs
Černá, Eva ; Mravec, Filip (referee) ; Pekař, Miloslav (advisor)
The aim of this paper is to discover whether it is possible to use the native form of hyaluronic acid as a hydrophobic drug carrier for a targeted distribution in the body. In its structure, hyaluronic acid is a linear high molecular weight biopolysaccharide which is found in most living organisms. Hyaluronan is involved in many physiological processes and therefore is essential for the functionality of the human body. It is in most tissues of the human body, high concentration is in the skin, the vitreous body and is also observed in cancer cells that contain several receptors for hyaluronan. These receptors include CD44 and RHAMM. The interaction of the hyaluronic acid delivery system and the hydrophobic medicinal with these receptors could ensure a free passage for drugs to the affected tissue, where the release of the drug would destroy the affected cells. The drug would directly target the damaged tissue and did not burden the rest of the body like the cytotoxic agents do. In this paper the native form of hyaluronic acid, which we normally find in the human organism, was chosen as the carrier. Its properties do not stand above other carrier systems, but its biocompatibility and biodegradability in the body greatly exceed them. High molecular weight hyaluronic acid was used as a carrier and the hydrophobic dye sudan red G, a substance of similar properties, was used instead of a hydrophobic drug.
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Gene regulation in four dimensions
Vaňková Hausnerová, Viola ; Lanctôt, Christian (advisor) ; Převorovský, Martin (referee) ; Krásný, Libor (referee)
Transcription has turned out to be a discontinuous process when imaged at a single cell level. This observation is referred to as transcriptional bursting or pulsing and has been detected in a variety of organisms ranging from bacteria to mammalian cells. The dynamics of transcriptional pulsing are influenced by the properties intrinsic to the transcriptional process, as well as by upstream factors: chromatin environment, signalling molecules, cell cycle stage etc. In the first part of this thesis, we focused on the regulation of transcriptional pulsing in the nucleolus. Using imaging of living cells, we detected pulsatile transcription of a transgene with nucleolar localization whose expression was mediated by RNA polymerase II. In the second part of the thesis, we investigated the relationship between chromatin decondensation and transcriptional dynamics. We used hyperosmotic medium to induce global condensation of chromatin and revealed that upon chromatin decondensation, a transient spike in transcriptional intensity occurs in induvial living cells. Next, we analysed expression of TFRC and POLR2A genes in several cell cycle stages using single molecule RNA FISH. We detected increase in both frequency and size of transcriptional pulses during a limited time window which coincided with chromatin...
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