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3D scanning of glossy surfaces
Zeman, Jakub ; Zatočilová, Aneta (referee) ; Koutecký, Tomáš (advisor)
The goal of this bachelor thesis is to experimentally determine the impact of different concentrations of titanium matte coating on the properties of matte film covering glossy surface intended for 3D scanning. Theoretical part of the thesis contains brief introduction to the 3D digitization of real objects as well as more detailed description of the particular scanning method used in this thesis and summary of possible digitizing errors and existing knowledge about matte coatings. The practical part composes of applying the titanium matte coating on specimens using automated coating device thus maintaining the exact same conditions for all concentrations. Following measurement of specimens using 3D scanner and optical profilometer results in determining the optimal concentration of titanium coating providing the best properties of the matte film.
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Experimental Assessment of Influence of Polyethylene Liners' Position on Plastic Deformation in the Run-in Phase of Wear
Zeman, Jakub ; Daniel, Matej (referee) ; Ranuša, Matúš (advisor)
The diploma thesis is focused on the run-in phase of total hip replacement. Mutual adjustment of contact surfaces takes place in this phase and polyethylene acetabular cup shows notable creep behaviour. The magnitude of creep deformations is assessed experimentally in relation to acetabular cups orientation in human body after its implantation. The condition of articulating surfaces is also assessed as well as resulting coefficient of friction in run-in phase. Physiological load and kinematics of the artificial joint as well as physiological conditioning is achieved by new module of existing joint simulator, which is created as part of this thesis. Deformations and condition of articulating surfaces are assessed via optical methods and SEM. Findings about the run-in phase are compared with existing FEM analyses to evaluate simplifications used in these analyses. Measurement of creep deformations has also potential to improve the accuracy of acetabular wear diagnosis in clinical practice.
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Novel hepatitis C virus proteins
Zeman, Jakub ; Vopálenský, Václav (advisor) ; Horníková, Lenka (referee)
The hepatitis C virus (HCV) is a major etiological agent of chronic liver diseases. More than 170 million people worldwide are chronically infected, and more than 100 thousand of them develop hepatocellular carcinoma a year. HCV is an enveloped, positive-sense single-stranded RNA virus (+ssRNA virus) of the family Flaviviridae. Its genome is translated to produce a single polyprotein precursor that is further processed by cellular and viral proteases to form 10 viral proteins. Moreover, there is another protein encoded in an alternative reading frame. Two alternative translation mechanisms have been proposed for expression of this alternative reading frame protein (ARFP): a frameshift mechanism and translation initiating from internal start codons. Despite ten years of research its role in vivo is not yet explained. It appears that secondary structures in the core encoding region of HCV genome but not ARFP expression are required for robust viral translation and replication. The results of recent studies suggest that mutations distorting these structures may result not only in slowing down the viral cycle but also in a brand new and utterly unusual serological profile in patients as well as an increased level of expression of ARFP.
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Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes
Zeman, Jakub
In eukaryotic translation, eukaryotic initiation factors (eIFs) are at least as important as the ribosome itself. Some of these factors play different roles throughout the entire process to ensure proper assembly of the preinitiation complex on mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most important factor integrating signals from others and coordinating their functions on the ribosome is eIF3. In Saccharomyces cerevisiae, eIF3 is formed by five subunits. All these subunits contain structural motifs responsible for contact with ribosomal proteins and RNAs. In addition to these highly structured parts, the rest of eIF3 is unstructured and very flexible. Therefore, despite the recent progress thanks to the use of a cryo-electron microscopy, a precise structure and position of eIF3 on the 40S ribosomal subunit are still not known. Also, the presence of eIF3 on 80S during early elongation and its role in reinitiation and readthrough are not fully understood. In order to crack mysteries of yeast eIF3, we used x-ray crystallography, chemical cross- linking coupled to mass spectrometry, and various biochemical and genetic assays. We demonstrated that eIF3 is very compactly packed when free in solution. This...
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Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes
Zeman, Jakub
In eukaryotic translation, eukaryotic initiation factors (eIFs) are at least as important as the ribosome itself. Some of these factors play different roles throughout the entire process to ensure proper assembly of the preinitiation complex on mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most important factor integrating signals from others and coordinating their functions on the ribosome is eIF3. In Saccharomyces cerevisiae, eIF3 is formed by five subunits. All these subunits contain structural motifs responsible for contact with ribosomal proteins and RNAs. In addition to these highly structured parts, the rest of eIF3 is unstructured and very flexible. Therefore, despite the recent progress thanks to the use of a cryo-electron microscopy, a precise structure and position of eIF3 on the 40S ribosomal subunit are still not known. Also, the presence of eIF3 on 80S during early elongation and its role in reinitiation and readthrough are not fully understood. In order to crack mysteries of yeast eIF3, we used x-ray crystallography, chemical cross- linking coupled to mass spectrometry, and various biochemical and genetic assays. We demonstrated that eIF3 is very compactly packed when free in solution. This...
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Binding of eIF3 in complex with eIF5 and eIF1 to the 40S ribosomal subunit is accompanied by dramatic structural changes
Zeman, Jakub ; Valášek, Leoš (advisor) ; Štefl, Richard (referee) ; Man, Petr (referee)
In eukaryotic translation, eukaryotic initiation factors (eIFs) are at least as important as the ribosome itself. Some of these factors play different roles throughout the entire process to ensure proper assembly of the preinitiation complex on mRNA, accurate selection of the initiation codon, errorless production of the encoded polypeptide and its proper termination. Perhaps, the most important factor integrating signals from others and coordinating their functions on the ribosome is eIF3. In Saccharomyces cerevisiae, eIF3 is formed by five subunits. All these subunits contain structural motifs responsible for contact with ribosomal proteins and RNAs. In addition to these highly structured parts, the rest of eIF3 is unstructured and very flexible. Therefore, despite the recent progress thanks to the use of a cryo-electron microscopy, a precise structure and position of eIF3 on the 40S ribosomal subunit are still not known. Also, the presence of eIF3 on 80S during early elongation and its role in reinitiation and readthrough are not fully understood. In order to crack mysteries of yeast eIF3, we used x-ray crystallography, chemical cross- linking coupled to mass spectrometry, and various biochemical and genetic assays. We demonstrated that eIF3 is very compactly packed when free in solution. This...
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Interactome of the translation initiation factor eIF4E2
Lettrich, Patrik ; Pospíšek, Martin (advisor) ; Zeman, Jakub (referee)
Regulation of gene expression at the level of translation is one of the most prominent processes when it comes to maintaining cellular vital functions in physiolgical norm. Initiation phase plays an especially important role in translational regulation. Majority of eukaryotic mRNAs possess methylguanosine cap on its 5' end. Binding of initiation factor eIF4E1 to cap is substantial part of canonical mechanism of translational initiation. eIF4E1 is component of bigger complex termed eIF4F, whose association with cap mRNA is essential for initiation of translation. Due to cap-binding ability of noncanonical initiation factors and their interaction partners, that are distinct from those of eIF4E1, there can occur specific regulation of translational initiation. One of these noncanonical factors is eIF4E2. In regulatory processes it mostly acts as a translational repressor. Binding of eIF4E2 to cap impedes association of eIF4F complex with mRNA, and therefore inhibits translation. However, eIF4E2 is also able to promote cap-dependent initiation of translation using an alternative mechanism in hypoxic conditions. This thesis represents the first complex analysis of protein-protein interactions and physiological functions of factor eIF4E2 and its homologs in several model organisms. Key words:...
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Experimental Assessment of Influence of Polyethylene Liners' Position on Plastic Deformation in the Run-in Phase of Wear
Zeman, Jakub ; Daniel, Matej (referee) ; Ranuša, Matúš (advisor)
The diploma thesis is focused on the run-in phase of total hip replacement. Mutual adjustment of contact surfaces takes place in this phase and polyethylene acetabular cup shows notable creep behaviour. The magnitude of creep deformations is assessed experimentally in relation to acetabular cups orientation in human body after its implantation. The condition of articulating surfaces is also assessed as well as resulting coefficient of friction in run-in phase. Physiological load and kinematics of the artificial joint as well as physiological conditioning is achieved by new module of existing joint simulator, which is created as part of this thesis. Deformations and condition of articulating surfaces are assessed via optical methods and SEM. Findings about the run-in phase are compared with existing FEM analyses to evaluate simplifications used in these analyses. Measurement of creep deformations has also potential to improve the accuracy of acetabular wear diagnosis in clinical practice.
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