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Preparation of fusion ligands and evaluation of their binding to NK cell receptors
Nepokojová, Tereza ; Vaněk, Ondřej (advisor) ; Grantz Šašková, Klára (referee)
Natural killer cells (NK cells) are an important part of innate immunity. On their surface they express a complex group of receptors that use different signalling motifs to activate or inhibit NK cell cytotoxic activity. NK cells are capable to kill aberrant cells (namely, viral, infected, and tumour cells) by using special cytotoxic mechanisms to trigger apoptosis. The activating receptors recognize tumour or stress-induced ligands, e.g., NKG2D receptor recognizes the MICA ligand and NKp30 recognizes the B7-H6 ligand. Therefore for human immune system it is only natural that cancer cells are destroyed by NK cells. The current therapeutic goals in the treatment of cancer are primarily focused on strengthening the body's own natural ability to fight with cancer and one possible way is stimulation of NK cells to win this deadly fight. In addition to NK cells, antibodies are also widely used for the treatment of cancer, as well as other immune-related disorders. Most of them are monoclonal antibodies, but antibody fragments are getting attention and are being tested more and more in recent years. This work describes the preparation of three bifunctional fusion proteins: B7-H6-L-aHER2, MICA-L-aHER2, and aHER2-L-MICA, which contain immunoligands for the activating receptors of NK cell and VHH fragment...
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Preparation of nanoparticles for hepatitis B viral therapy
Kružíková, Zuzana ; Grantz Šašková, Klára (advisor) ; Žáčková Suchanová, Jiřina (referee)
Hepatitis B virus (HBV) represents one of the hot topics of current basic and pharmaceutical research. Although an effective vaccine against HBV exists since 1982, the world prevalence of chronic infection is still alarming. The infection can lead to significant liver damage, often resulting in hepatocellular carcinoma. Chronic HBV infection cannot be cured due to the fact that the viral genome persists in the infected hepatocyte hidden from the host immune response as well as from the antiviral treatment. One of the novel approaches aiming for HBV cure suggests that this cccDNA pool could be destroyed using gene editing tools such as CRISPR/Cas9 system. In order to shift this gene editing system to possible medicinal application, CRISPR/Cas9 has to be specifically delivered into the target cell in order to minimize its putative off-target activity. This thesis focuses at first on the design and efficacy testing of new sgRNAs targeting HBV cccDNA and secondly, it describes modular lipid nanoparticles developed specially for delivery of the CRISPR/Cas9 system in the form of RNA. Keywords: hepatitis B virus, CRISPR/Cas9, gene editing, lipid nanoparticles, mRNA delivery, targeted delivery
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Bacteriophage therapy with focus on urinary catheters biofilms
Ludvík, Vojtěch ; Drda Morávková, Alena (advisor) ; Grantz Šašková, Klára (referee)
The term of the bacteriophage therapy denotes the use of viruses for killing bacteria. My thesis refers about the use of the bacteriophage therapy in the process of treating nosocomial infections caused by the urinary tract catheterization. I focus on the bacteria that are found in the catheters' biofilms and on the selection of bacteriophages that will be capable of the enzymatically degradation of the biofilms as well as the lysis of the present bacteria. After the body fluids contact the surface of the catheter, an environment for the evolution of the biofilm begins to evolve, which leads to its fast expansion and to the development of an infection. In the case of improper hygienically measures and unreasonable duration of the catheterization, the incidence of the infections reaches 100%. Because of the presence of the biofilm, the bacteria demonstrate high resistance to antibiotics, which is why the infections often aren't suppressed and may have fatal consequences. If applied, the bacteriophage cocktail and genetically modified bacteriophages can successfully treat the infection and even prevent from its development. Keywords: Bacteriophage therapy, urinary tract infection, catheterization, biofilm, EPS
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Searching for a physiological partner of Ddi2 (DNA damage-inducible protein homolog 2) protein
Kurfürst, Jaroslav ; Grantz Šašková, Klára (advisor) ; Vaněk, Ondřej (referee)
One of the most important cellular processes, essential not only for protein degradation, is the so called ubiquitin-proteasome system. A key player in this system is ubiquitin, a small protein with unique ability to form various chains. Cellular proteins marked for degradation via ubiquitin, are recruited to the proteasome either by a direct interaction with one of the intrinsic proteasomal receptors, or by adaptor proteins. These proteins typically possess ubiquitin-like domain and ubiquitin associated domain that predispose them for delivering ubiquinated proteins to the proteasome. Adaptor protein called Ddi2 differs from other members of this family by possessing additional domain called the retroviral protease like domain. This domain is structurally similar to HIV protease and its proteolytic function has been discovered only recently. Due to the presence of this proteolytic domain one could expect that Ddi2 might be a deubiquitinase. Here we therefore tested the possible cleavage of diubiquitin chains by recombinantly prepared Ddi2 protein. We can conclude that Ddi2 did not show any deubiquitinating activity in given conditions.
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Ddi1-like proteins: a novel family of retroviral-like aspartyl proteases
Šmilauerová, Kristýna ; Grantz Šašková, Klára (advisor) ; Šmahel, Michal (referee)
Ubiquitin-proteasome system is one of the key pathways which maintain cell homeostasis. Its purpose is to degrade damaged, misfolded or unnecessary proteins. It is also involved in multiple other processes such as DNA damage repair, cell cycle control or signaling. The entire system consists of multiple components, which are mutually strictly regulated. Important part of this system is group of so called proteasome adaptor proteins. Their role is to recognize and bind targeted substrates and transport them to the proteasome for degradation. Ddi1-like (abbrev. from DNA damage-inducible protein 1) protein family, a group of proteins with retroviral aspartyl protease-like domain, belongs to proteasome adaptor proteins. Global biological role of this protein family is only partially understood the most studied member is Ddi1 protein from Saccharomyces cerevisiae, and it is thus a subject of active research. This thesis summarizes published information about this protein family, describes its general characteristics and known functions, situates them in the context of cell processes and thereby might suggest the course of further study.
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Structure determination of helical domain of DNA damage-inducible protein 2
Staníček, Jakub ; Grantz Šašková, Klára (advisor) ; Obšil, Tomáš (referee)
Human Ddi2 and his homologues are scarcely explored family of ubiquitin- like/ubiquitin-associated domain proteins (UBL/UBA proteins), containing domain which is structurally related to dimeric aspartyl proteases from retroviruses. The most studied of this family is Ddi1 protein from Saccharomyces cerevisiae, which functions within the ubiquitin- proteasome system. This key cellular system exploits tightly regulated enzymatic apparatus for highly selective posttranslational modifications of proteins with molecules of ubiquitin, which serves as intracellular signal determining the proteins fate, importantly its degradation in many cases. Ddi1 plays a role of proteasome adaptor within this context, helping the recognition of ubiquitylated proteins by the proteasome. Even though the function as a proteasome receptor is possible for human Ddi2 protein as well, its cellular role might have been altered during the evolution. One of the important steps in decoding its purpose in cell is exploration of function of its individual domains. This work focuses on structural study of neighbouring region of this protease domain, where the helix-rich region called HDD domain is located. This region of Ddi2 was cloned, expressed and subjected to the NMR measurements. Structural information based on the NMR data was...
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Nanoparticles for gene editing
Kružíková, Zuzana ; Grantz Šašková, Klára (advisor) ; Beranová, Jana (referee)
Early DNA-based therapies were tested for therapeutic applications, but they sooner or later revealed multiple hurdles and risks preventing their use in further clinical trials. Recently, they have been replaced by rapidly evolving gene editing using programmed nucleases capable of precise genome modifications by cleaving specific DNA sequences. Zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and CRISPR/Cas9 system are currently under investigation as potential therapeutics. However, their off-target effects must be controlled. Targeted delivery of nucleases in a form of mRNA seems as the most promising method. Various types of nanoparticles enable mRNA transfer and could be used to facilitate the nuclease application. Some of these nanoparticles together with characterization of the programmed nucleases are described in this thesis.
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DNA damage-inducible protein: interaction partners and potential role in proteasomal degradation
Belza, Jan ; Grantz Šašková, Klára (advisor) ; Vaněk, Ondřej (referee)
Ddi1-like proteins (DNA damage-inducible) have been so far best characterized in yeast (Ddi1 protein from Saccharomyces cerevisiae), drosophila and quite recently also in human (Ddi2 protein). Based on their domain architecture they belong to the family of proteasomal shuttle proteins that transport ubiquitinated proteins for proteasomal degradation. They contain ubiquitin-associated domain (UBA) responsible for the interaction with proteasome subunits and ubiquitin-like domains (UBL) required for the interaction with ubiquitinated proteins. However, they also seem to have other functions. The yeast homolog Ddi1 is involved in cell cycle control, plays a role in the degradation of HO endonuclease and probably also functions as a negative regulator of exocytosis. The cellular functions of recently identified human homolog Ddi2 are not yet understood. In order to contribute to the understanding of the physiologic functions of human Ddi2 protein, we decided to identify potential binding partners of this protein. Therefore, we prepared DNA constructs for the expression of Ddi2 in mammalian HEK293 cells fused to two affinity tags, either FLAG or HA or Myc tag, that enable their facile visualisation and purification. Affinity chromatography coupled to mass spectrometry (AP-MS) aided in identifying...
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The effect of iron on the metabolism of the protozoan Trypanosoma brucei
Arbon, Dominik ; Konvalinka, Jan (advisor) ; Grantz Šašková, Klára (referee)
Iron ions are essential components of numerous cell processes. Their utilisation is strictly regulated, since any impairment can have devastating effect on the cell. In living organisms, iron ions are bound to proteins, for storage, transportation, or as a vital part of catalytic centers of enzymes. Transportation of iron ions between different compartments is important for the correct function of the cell. It was recently shown on yeast, how a mitochondrial transporter of iron ions is essential for the synthesis of iron-sulfur clusters of enzymes. This work aims to describe the localization and function of a homologous protein of a parasitical organism Trypanosoma brucei, which causes African trypanosomiasis, also known as sleeping sickness. This parasite is entirely dependent on uptake of iron ions from its host and therefore the utilization of iron ions is studied as a potential therapeutic target. This work is focused on the characterization of protein Mcp17, which is assumed to function as a transporter of iron ions into the mitochondria of T. brucei. Utilizing expression of marked Mcp17, the transporter was confirmed to be localized on the mitochondrial membrane of the cell. Measuring of enzyme activity of selected enzymes indicated that cells with inhibited expression of the gene mcp17...
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HIV - 1 Protease: Insights into Drug Resistance Development
Grantz Šašková, Klára ; Konvalinka, Jan (advisor) ; Forstová, Jitka (referee) ; Dohnálek, Jan (referee) ; Schiffer, Celia (referee)
Amino acid changes within HIV protease or its substrate that decrease the susceptibility to protease inhibitors represent a highly complex issue still not yet fully understood. Various mechanisms by which this often complicated pattern of mutations influence drug binding needs to be analyzed on a molecular level by a series of methods including experiments with recombinant viruses, biochemical enzyme analysis, structural and thermodynamical studies or molecular dynamics. Each result may help to complete the overall picture of protease inhibitor resistance evolution and therefore contribute to the design of more powerful 3rd generation HIV/AIDS drugs. This thesis presents several analyses of HIV resistance development on molecular level. We have focused on the nelfinavir resistance pathway, lopinavir mutation score, emergence of amino acid insertions in HIV protease gene and their contribution to protease inhibitor resistance and finally we analyzed a highly mutated protease species isolated from patients failing darunavir therapy. Since we are able to accomplish a wide combination of techniques, we could explain and put together some pieces of viral evolution considering the final steps of HIV life cycle and also provide knowledge necessary for novel inhibitor design. Aims of the Project There were...
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