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Leaf physiological and optical properties in relation to the Phytophtora × alni infection of black alder (Alnus glutinosa)
Oramová, Viktorie ; Lhotáková, Zuzana (advisor) ; Tomášková, Ivana (referee)
A current problem is the infestation of the black alder (Alnus glutinosa) by the pathogen P. × alni, which causes the loss of alder stands and disrupts riparian ecosystems. The spread of the 'phytophthora disease' occurs through water, the host is infected through the root system and the pathogen attacks the conductive tissues. As a result of the disease, the tree gradually loses its root system, lesions appear on the trunk, defoliation occurs and the individual inevitably dies. The only solution to the situation is preventive measures to prevent further spread by careful removal of infected alder trees. The aim of this paper is to discuss the relationship between black alder and P. × alni in the context of the physiological changes that occur in the foliage of the infested individual. Leaf functional traits, chlorophyll fluorescence and optical properties of black alder exposed to P. × alni (inoculation into soil or confirmed occurrence of the pathogen in natural conditions) were measured using non-invasive methods. The results of the chamber experiments suggest that the mean values of the measured parameters do not change significantly in the initial stages of infection, but there is a widening of the variance of the values in infected individuals. We tested whether the genetic origin of the...
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Novel therapeutic targeting of the quorum sensing transcriptional regulation in multi-antibiotic resistant bacterium Staphylococcus aureus
Maďarová, Anna ; Maloy Řezáčová, Pavlína (advisor) ; Cherepashuk, Ivan (referee)
The threat of antibiotic resistance is deemed as a ticking time-bomb, yet in spite of this, the number of newly discovered antibiotics continues to steeply decline. Each year, infections caused by multi-drug resistant bacteria kill more than 4.95 million people, which demonstrates that in order to tackle this crisis, a novel approach is desperately required. The solution could be found in targeting bacterial transcriptional regulators that are responsible for the control of various virulence factors and can be highly species-specific. This also applies to the most widespread multi-drug resistant bacterium Staphylococcus aureus, whose virulence is intricately linked to the transcriptional regulation of the quorum sensing system. The aim of this bachelor thesis is to summarize current knowledge about clinically relevant transcriptional regulators that are associated with this system (AgrA, SarA, SarR, MgrA, Rot), with focus on their 3D structures, mechanisms of action, and inhibition. Key words: antibiotic resistance, transcriptional regulation, quorum sensing, Staphylococcus aureus
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Algorithms for integration of single-cell transcriptomic data
Ševčovičová, Zuzana ; Kolář, Michal (advisor) ; Abaffy, Pavel (referee)
Single-cell transcriptomics represents an innovative technique that allows for the examination of gene expression of individual cells in tissues or other complex biological samples. The data gen- erated through this approach offer crucial insights into various biological domains, such as em- bryology, oncology, and immunology. Understanding the functioning and mutual interactions of individual cells within tissues indeed requires knowledge of their individual expression profiles. Given the novelty of this method and technical challenges faced during data generation, com- parison of different samples may be difficult and affected by various batch effects. Effectively reconciling the information obtained regarding gene expression in distinct biological replicates or technical replicates generated by different methodologies may be onerous. The development of bioinformatics approaches to address this challenge is an ongoing process. The objective of this thesis is to: 1. survey the existing solutions for integration of single-cell transcriptomic data, 2. benchmark these solutions using publicly available datasets, specifically peripheral blood mononuclear cells, and 3. select the most suitable integration method to apply to a tumour microenvironment dataset generated by our laboratory. This bachelor...
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Analysis of anti HLA antibodies using luminex (XMAP) methods in patients before and after kidney allotransplantation
Holoubková, Renata ; Jankovičová, Karolína (advisor) ; Andrýs, Ctirad (referee)
This work focuses on mastering the technique of examining anti-HLA antibodies using the multiplex Luminex method. The aim was to become proficient in working with analytical software capable of evaluating the specificity and levels of individual anti-HLA antibodies in patients' sera before and after kidney transplantation. Additionally, cut-off values for screening for anti-HLA antibodies in the assessed patient cohort were determined. Furthermore, an analysis of sensitization to individual HLA antigens was performed in a group of patients with low antibody levels. In the theoretical part of this work, I addressed the major histocompatibility system (HLA system) and its significance in transplantology. I also focused on the issues of transplant immunity and the principles of alloreactivity and rejection. I discussed the origin and significance of HLA antibodies and examined various methods for analyzing anti-HLA antibodies, particularly the multiplex Luminex method. In the experimental part, conducted at the Department of Clinical Immunology and Allergology in Hradec Kralove, I analyzed antibodies targeting HLA class I and II antigens using the multiplex Luminex method. Screening index values were monitored for both HLA classes. In subsequent typing examinations, MFI values were observed for...
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Plant defence against arsenic toxicity: a key role of arsenate reductase?
Jurčíková, Martina ; Mašková, Petra (advisor) ; Hála, Michal (referee)
Arsenic in its various forms is one of the most toxic environmental contaminants, which is also taken up by plants and can affect their vitality. The risk category is crops where As contamination reduces the overall yield and through which As enters the food chain. Its inorganic (arsenite and arsenate) and organic (methylated) forms are taken up by roots and rhizomes, where they can either accumulate or be translocated and subsequently stored in shoots. Arsenate reductase is an enzyme that catalyses the reduction of arsenate to arsenite, thereby affecting not only the overall toxicity of As in the plant, but also its transport between underground and aboveground organs. However, the interplay of the different mechanisms of As uptake, translocation and detoxification has not been investigated in detail. The aim of this bachelor thesis was to analyze and compare the importance of arsenate reductase in these processes in the model organism Arabidopsis thaliana, in a rice crop and in the arsenic hyperaccumulator Pteris vittata. The different tolerance of these organisms to As and their differences in the preferential site of As deposition in leaves or seeds could be used for different purposes, such as in the phytoremediation of As-contaminated soils, or in limiting the uptake or translocation of As to...
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Inquiry-based education focused on traffic noise pollution
Gonzálezová, Natálie ; Jelen, Jakub (advisor) ; Matějček, Tomáš (referee)
The bachelor thesis focuses on teaching the impacts of traffic in grammar schools. Specifically, it addresses one of the leading negative impacts, namely noise pollution, which is a worsening problem as the volume of traffic continues to grow. The aim of the thesis is to create and implement a lesson on this topic using an inquiry-based teaching approach. Pupils will learn how to measure approximate noise levels, understand its impacts, and devise a plan to improve the situation. The lesson will be pilot tested by pupils from the Secondary School of Surveying and the Geographical Grammar School in Prague. The theoretical part introduces the issue of noise pollution in more detail, describes inquiry-based teaching and its integration into lessons. The practical part provides teaching materials and a thorough methodology, that serves as a guide for teachers who would like to apply the lesson in their classes. Subsequently, the course of the lesson at the Geographical Grammar School is described, along with reflections from both the teacher's and students' perspectives. Based on assessment of the students' knowledge before and after the lesson, they appeared to have a better understanding of the issue. In the feedback, the pupils especially appreciated the fieldwork, the formation and testing of...
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Molecular mechanisms of Bardet-Biedl Syndrome
Mašková, Kristýna ; Huranová, Martina (advisor) ; Doubravská, Lenka (referee)
Bardet-Biedl Syndrome (BBS) is a rare genetic disease categorized under ciliopathies; a group of diseases linked to primary cilia dysfunction. Primary cilia, also known as cellular antennae, play a vital role in sensing extracellular stimuli and transducing them through various signalling cascades. Proper cilia function and signalling depends on multiple ciliary proteins, with eight of them forming a BBSome complex. The BBSome is involved in the transport of proteins into and out of the cilia. Mutations in genes encoding BBSome complex lead to BBS. Among these genes, BBS1, which encodes the BBS1 subunit of the BBSome, is notably highly mutated compared to others. This thesis focuses on the BBS1 subunit and aims to investigate the molecular mechanisms underlying three specific BBS patients' mutation located in BBS1: M390R, E224K, R160Q. In the first part, we validated the expression of these selected BBS1 variants and examined their effects on the expression of other BBSome subunits. We observed decreased expression levels of BBS4 and BBS5 subunits in the presence of M390R and E224K mutations. Secondly, we assessed BBSome assembly in the context of these mutations, showing that R160Q mutation did not impair BBSome assembly, whereas assembly was severely disrupted in the presence of M390R variant,...
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Mechanisms of membrane protein quality control in the endoplasmic reticulum
Jirout, Matěj ; Stříšovský, Kvido (advisor) ; Bařinka, Cyril (referee)
Integral membrane proteins (IMPs) undergo extensive quality control (QC) within the endoplasmic reticulum (ER) to maintain ER proteostasis and the integrity of the ER proteome. ER-associated ribosome quality control (ER-RQC) responds to ribosome stalls during translocation and helps "de-clog" blocked translocon. ER-associated degradation (ERAD) targets misfolded IMPs for proteasomal degradation. ERAD-resistant IMPs are degraded by different ER-phagic pathways, collectively referred to as ELRAD (ER-to-lysosome associated degradation). Coordination of these mechanisms is facilitated by the unfolded protein response (UPR), although UPR receptors are most likely not activated by aberrant IMPs, as all these mechanisms function in the QC of ER-luminal proteins.
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Silencing of Transposable Elements in Plants and Implications for Rationalised Transgene Design
Tobiáš, Andrej ; Fischer, Lukáš (advisor) ; Moravec, Tomáš (referee)
(English) Transposable elements (TEs) are integral parts of all plant genomes. Their ability to change their position (transpose) or copy to a new position and induce mutations within these genomes has driven evolution for billions of years. Despite its importance, unrestrained transposition can lead to irreversible genomic damage. Therefore, plants have evolved special silencing mechanisms to regulate transposition and "silence" TEs. This allows plants to harness the mutagenic potential of TEs, tame their new insertions, and thus potentially acquire genomic novelties. Silencing mechanisms operate mostly at the epigenetic/transcriptional level, where they induce methylation on target DNA or histones. This accounts for RNA-dependent DNA methylation pathways (RdDMs). Additionally, they operate at the post-transcriptional level, where they degrade target mRNA through a pathway known as post-transcriptional gene silencing (PTGS). These silencing mechanisms have also become proficient in recognizing both natural and artificial transgenes. Recognition and subsequent silencing of transgenes diminishes the efficiency of transgenesis and, thus, successful production of genetically modified organisms (GMOs). Extensive research into these silencing pathways and TEs can lead to a better understanding of what...
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The period of the Third Czechoslovak Republic in the context of international agreements and international politics
Czapek, Alexandr ; Kuklík, Jan (advisor) ; Blažek, Lukáš (referee)
The Third Czechoslovak Republic Period in the Context of International Contracts and International Politics This thesis titled "The Third Czechoslovak Republic Period in the Context of International Contracts and International Politics" is divided into a total of five chapters. In the first chapter, or rather in its theoretical part, the author first defines the observed period of 1938-1948 and then defines the legal institutes with which he works in the thesis. In the second chapter of the thesis, the author describes the period of the so-called Second Republic and its political development. In the third chapter of the diploma thesis, the author describes the activities of the Czechoslovak authorities in foreign exile. In this chapter, he discusses the steps of the foreign resistance directing the Czechoslovak government in exile and the process leading to the denunciation of the Munich Agreement. In the last part of this chapter, the author discusses the influence of communist members of parliament on foreign resistance, the improvement of relations with the Soviet Union, President Beneš's visit in Moscow and the negotiation of an alliance agreement between Czechoslovakia and the USSR. In the fourth chapter of the diploma thesis, the author deals in detail with the so-called Potsdam Conference....
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