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Visualization of Marked Cells of a Model Organism
Kubíček, Radek ; Kršek, Přemysl (referee) ; Herout, Adam (advisor)
This master thesis is focused on volumetric data rendering and on highlighting and visualization of the selected cells of the model organisms. These data are captured by a confocal deconvolution microscope. Input data form one large volumetric block containing separate slices. This data block is rendered by an applicable method and then are identified and visualized the cells marked by the GFP (Green Fluorescent Protein) process or by chlorophyle fluorescency. The principal aim of this work is to find out the preferably optimal effective method enabling this highlighting, most preferably working without a manual check. Due to the data structure, this ambition seems hardly realizable, so it suffices to find out a manual working method. The last step is to embed the results of this work into FluorCam application, the confocal deconvolution microscope data visualizer.
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Mechanical forces in asymmetric cell division
Šabata, Vojtěch ; Macůrková, Marie (advisor) ; Middelkoop, Teije Corneel (referee)
Cell division is one of the most studied topics in the field of cellular and molecular biology. In some cases, cells can exploit diverse mechanisms to alter the basic function of their division machineries to divide asymmetrically. This results in two daughter cells that differ from each other in some manner, which is an essential premise for the development and adult homeostasis of complex multicellular organisms. This work is focused on the division of Caenorhabditis elegans zygote, a classic example of asymmetric division. Using this model system, this work highlights the cellular mechanisms used to generate polarity, with emphasis on the purely mechanical aspects present. In recent years, great progress has been made in describing these fundamental pathways, which are at their core highly conserved from nematodes to humans. Deeper knowledge of processes, that are responsible for a successful cell division in general, can be beneficial for a better understanding of organismal development in health and disease.
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Preparation of the constructs for analysis of expression of nuclear receptor nhr-97 by using transgenic techniques in the model system Caenorhabditis elegans
Boušová, Kristýna ; Stiborová, Marie (advisor) ; Hudeček, Jiří (referee)
The aim of this work was to prepare two constructs of the promoter of a gene coding for nuclear hormone receptor nhr-97 in C. elegans. Nuclear receptors belong to a large group of genes sharing homologous sequences in some vertebrate nuclear receptors. The first part of the work describes the structure of nuclear hormone receptors, their function and significance in the nematodes C. elegans. The model organism C. elegans, its anatomy, life cycle and genome were also described. The work also discusses the structure and use of green fluorescent protein (GFP), which serves to localize the expression of the nhr-97 gene in C. elegans. In the practical part of the work, the preparation of two constructs of the promoter is described. Isolation of genomic DNA of C. elegans, PCR amplification of the promoters and their subsequent cloning into vector pPD95.67 containing a gene coding for green fluorescent protein were performed. To verify the successful cloning of the promoter constructs, sequencing DNA was performed. Cloned promoters of nhr-97 will be used for microinjetions to C. elegans gonads and the expression of this gene regulated from particular promoters will be subsequently monitored using expression of green fluorescent protein in progeny.
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The role of CUP-4 protein in Wnt signalling
Žídek, Radim ; Macůrková, Marie (advisor) ; Pospíchalová, Vendula (referee)
Wnt signalling is indispensible for proper development of organisms and maintaining of adult tissue homeostasis. Its disruption often leads to disease. In nematode Caenorhabditis elegans, Wnt signalling governs vast array of developmental processes, among others also migration of the Q neuroblasts and their descendants. The sole Wnt acting in this process, EGL-20, triggers the canonical β-catenin Wnt signal transduction pathway in QL but not in QR which leads to QL remaining in the posterior while the QR migrates anteriorly. This represents a useful tool for studying Wnt signalling. Recently, mutation of gene cup-4 was found to disrupt migration of the QL neuroblast in a small proportion of the mutant population. cup-4 encodes a ligand-gated ion channel family homologue and it was shown to participate in endocytosis by coelomocytes, specialized phagocytic cells in the C. elegans body cavity. Here, I present the results of my effort to determine the place of CUP-4 action in Wnt signalling and to elucidate the mechanism of its function. I found that CUP-4 acts upstream of PRY- 1/Axin, which is involved in signal transduction in signal receiving cells, and most probably downstream of adaptin AP2, which is important for recycling of Wnt cargo receptor Wntless (Wls) in Wnt producing cell. cup-4 also...
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Regulation of protein expression non-specific immunity in Caenorhabditis elegans
Kaštánková, Iva ; Kostrouch, Zdeněk (advisor) ; Cmarko, Dušan (referee)
6 Abstract Lipopolysaccharides are composed of covalently bound saccharides. They are a characteristic component of the cell wall of gram-negative bacteria. They are the cause of severe sepsis in humans and complications in human medicine. Lipopolysaccharides are a constant part of the infections of gram-negative bacteria. We expect an evolutionarily conserved non-specific immune response and protection. The question is whether there is an immune response in the model organism Caenorhabditis elegans. If so, what mechanism is controlled and regulated. We submitted lipopolysaccharides from the bacteria Pseudomona aeruginosa with the bacteria Escherichia coli OP50 and observed the influence of lipopolysaccharides on the expression of selected genes. We examined metabolism and development. We have shown the influence of lipopolysaccharides on gene expression of C-type lectine clec-60 a clec-71, nextna lys-5, hsp-60 a F44G.3.2.1 genes. We incubated Caenorhabditis elegans on some components of lipopolysaccharide. We found regulation of these selected genes with hydrophobic components of lipopolysacharide, lipid A. We did not observe regulation with saccharide components of lipopolysaccharide, glucose and galatose. The metabolism of lipids had changed. We demonstrated a reduction of neutral lipids and changes in...
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Study of expression of the nuclear receptor nhr-97 in Caenorhabditis elegans
Boušová, Kristýna ; Stiborová, Marie (advisor) ; Vaněk, Ondřej (referee)
Nuclear hormone receptors (NHR) are important transcription factors that regulate development and metabolism in the large group of animals. Caenorhabditis elegans contains 284 nuclear receptors, which is unusually large amount compared to receptors of Drosophila melanogaster (18) and humans (48). 15 receptors of the C. elegans have homologous receptor structure with receptors of D. melanogaster and mammals. The remaining 269 NHR are specific to nematodes and belong to the group of supplementary nuclear receptors (SupNRs), the evolutionary precursor of the HNF4 - an important transcription factor in humans. In this work we describe the nuclear hormone receptor nhr-97 C. elegans, whose expression and function have not yet been studied. The gene is encoded in the genome of C. elegans and is among SupNRs. Nhr-97 consists of two isoforms A and B, whose expression in C. elegans tissues is different. Localization of gene expression in vivo was determined using lines expressing nhr-97:: GFP. For the A isoform expression of nhr-97::GFP was localized in neurons in the pharynx and the tail, in the intestine and hypodermis, in isoform B in the pharynx, in neurons around the corpus of pharynx, the head mesodermal cell and in anal sphincter. Nhr-97 expression during development of C. elegans was determined by...
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Gene expression regulation by nuclear receptors in a specific metabolic context - evolutionary perspective
Kaššák, Filip ; Kostrouch, Zdeněk (advisor) ; Macůrková, Marie (referee) ; Leontovyč, Ivan (referee)
In animals, some of the most critical regulators of gene expression are nuclear hormone receptors (NRs) and their coregulators, specifically the Mediator complex. Of particular interest are the NRs implicated in metabolic and developmental regulation and in carcinogenesis: thyroid hormone receptors (TRs) and retinoid X receptors (RXRs). In this work, I venture to elucidate some aspects of gene expression regulation by these NRs: the degree of evolutionary conservation of signalling based on NRs and their coregulators; the mechanisms of negative regulation by NRs; and possible implications of these findings for clinical medicine. State-of-the-art bioinformatical, genome editing and microscopic techniques are applied at three levels of animal evolution to study NRs and Mediator. Reverse genomics in human patients suffering from the syndrome of resistance to thyroid hormones β are used to infer the structure and function of TRβ subdomains. Alignments, binding studies and in vivo experiments in Trichoplax adhaerens allow identification of a close orthologue of human RXR at the basis of metazoan evolution. Employing database queries, genome editing and microscopy, we describe a correct orthologue of the Mediator subunit 28 in Caenorhabditis elegans, indicating a complete homology of the Mediator complex...
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The role of phosphatidylinositol-4-phosphate 5-kinase PPK-1 in Wnt signalling regulation in Caenorhabditis elegans
Zavadilová, Kristýna ; Macůrková, Marie (advisor) ; Kostrouch, Zdeněk (referee)
The Wnt signalling pathway is highly conserved signalling among Eukaryotes that regulates many cellular processes. In particular, it plays a role during invidual's development, but it is also important at later stage of life, when it is involved in maintaining homeostasis in the body. Recent studies have shown that phosphatidylinositol-4-phospahte 5-kinase (PIP5K), which is key to the production of phosphatidylinositol (4,5)-bisphosphate in the cell, is also involved in regulation of the canonical Wnt signalling cascade. In mammalian cells, a model has been described in which PIP5K is involved in signal transduction in a Wnt receiving cell. We decided to verify the involvement of PIP5K in the regulation of Wnt signalling also in Caenorhabditis elegans, an excellent model organism for study of signalling pathways, and thus contribute to a better understanding of this evolutionarily conserved pathway. In this work, we found that decreased expression of PPK-1/PIP5K in wild type animals does not result in Wnt signalling disruption. Nevertheless, in conditions, where the activity of Wnt signalling is already reduced, decrease in PPK-1 levels leads to defective migration of the QL neuroblast daughter cell. By analyzing the migration of QL progeny, which is controlled by EGL-20/Wnt dependent Wnt...
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Nuclear receptors in regulation of gene expression, development and metabolism in Celegans elegans.
Yilma, Petr ; Kostrouch, Zdeněk (advisor) ; Pompach, Petr (referee) ; Vaněk, Ondřej (referee)
5 Abstract Genetic mechanisms of regulation of gene expression form the basis for proper development, function of organisms and their responses to variable life conditions. However, they are relatively slow. Life processes that require a fast response to the changing environmental and metabolic conditions are mostly executed on the level of proteins especially their posttranslational modifications and protein- protein interactions.The goal of the experimental work that led to the presented thesis consisted in exploitation of the model organism Caenorhabditis elegans for analysis of regulation of gene expression by transcription factors from the protein family of nuclear receptors. The model system C. elegans enables very efficient experimental procedures in the field of genetics, genomics and functional analysis of phenotypes. In the experimental work connected with this thesis, I studied the regulation of gene expression under specific experimental conditions from the perspective of advanced functional proteomics and I focused on the employment of separation methods and methods of advanced proteomics, especially by mass spectrometry.In the first part of the work, I characterized the nuclear receptor NHR-60 on the protein level. This nuclear receptor is expressed as two protein forms with a mass of 50 kDa...
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Evolutionarily conserved mechanisms of gene expression regulation by nuclear receptors.
Chughtai, Ahmed Ali ; Kostrouch, Zdeněk (advisor) ; Malínský, Jan (referee) ; Brábek, Jan (referee)
Transcriptional regulation of gene expression in eukaryotes has evolved over millions of years. The regulatory pathways of nuclear receptors represent an evolutionarily ancient, but conserved mechanism with associated accessory proteins, many of them forming a functional nexus known as the Mediator complex involved in transcription. Despite the versatility of the pathway, e.g. through the adoption of new regulatory functions in phylogenetically more recent Metazoa, we hypothesise that the intrinsic potential of the NR-Mediator axis to directly translate a stimulus to a biological response is conserved across species, and additional regulation could also be achieved through secondary functions of its essential members. To support the hypothesis, we assessed the ligand-binding capability of retinoic X receptor in Trichoplax adhaerens and provided evidence to support the concept that this capability was already present at the base of metazoan evolution. With regards to the potential secondary functions, we took inspiration from previous research and identified the Mediator subunit 28 (MED28) as the only known member having documented nuclear and cytoplasmic dual roles, and thus possessing the potential to transmit signals from the cellular structural states to the nucleus. Due to the lack of...
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