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Comparison of effectiveness of teaching using computers vs. 3D models
Andělová, Denisa ; Janštová, Vanda (advisor) ; Jáč, Martin (referee)
Currently, pupils' interest in science continues to decline, although this area of education is very important in every day life (medicine, environment, etc.) and there is high demand for science professions on the labor market. Molecular biology curriculum concerning DNA and the transfer of genetic information is abstract and difficult topic for pupils to imagine, and for teachers to explain. There are many ways to teach this topic. Very popular are iquiry and laboratory practise. But not all schools have their own laboratories, and can teach molecular practical effectivelly. Inquiry based teaching is time consuming to prepare, and not every topic is appropriate to be taught this way. Another possibilities how to visualize "invisible" molecules and processes are computer software and animations or 3D physical model. In my thesis, I examined the effect of using computers and animations to teach abou DNA compared to using a 3D physical model on students' knowledge. I laso tested the possible influence of gender and pupils' preferences on their achieved score on knowledge tests. The research was performed in five classes at three high schools in Prague. Students in year 12 were on different types of high school and some of them took special biology class, their age was between 15 and 18 years. The...
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Characterization of the molecular mechanism of translation reinitiation in yeast.
Pondělíčková, Vanda ; Valášek, Leoš (advisor) ; Hašek, Jiří (referee) ; Vopálenský, Václav (referee)
Translation initiation is a multi-step process culminating in formation of the elongation- competent 80S ribosome. It requires accurate assembly of small and large ribosomal subunits, mRNA, initiation Met-tRNAi Met and at least 12 eukaryotic initiation factors (eIFs). This phase of protein synthesis is also one of the key points of regulation of gene expression. One of the main aims of our laboratory is a complex characterization of the multiprotein eIF3 complex that has been implicated in most of the steps of translation initiation. For example, we revealed and described its novel role in translation reinitiation (REI), a gene-specific translational control mechanism that among others governs expression of an important yeast transcriptional activator GCN4. Here I present a detailed characterization of the multi-functional N-terminal domain of Tif32 (subunit eIF3a). We demonstrated that the Tif32-NTD functionally interacts with the 5' sequences of short upstream ORF (uORF1) in the GCN4 mRNA leader and thus allows efficient reinitiation downstream of this critical reinitiation-permissive uORF. Four REI- promoting elements (RPEs) were identified in the 5' sequences of uORF1, two of which were shown to work in the Tif32-NTD-dependent manner. The structure of the 5' sequences was determined...
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Cell death-regulating micro RNAs and their role in the development and pathological processes.
Běhounek, Matěj ; Anděra, Ladislav (advisor) ; Seifertová, Eva (referee)
MicroRNAs are small protein non-coding, ~ 22 nucleotides long dsRNAs. Their main task is suppression of gene expression via removal/destabilization of mRNA or its targeting to degradation. These small molecules play an important role in the regulation of many cellular processes and have been found to affect expression of more than 30% of human genes. Among the processes affected or regulated by miRNAa belongs also programmed cell death. Although this work is mainly focused on the analysis and characterization a role of distinct miRNAs in the regulation of apoptotic cell death, miRNAs can also participate in the regulation of autophagic cell death or programmed necrosis. MiRNA can enhance cellular sensitivity to apoptosis by suppressing the expression of death receptor genes, but can also drive cells to apoptosis by regulating expression of anti-apoptotic protein Bcl-2. In many different organisms were already discovered and described thausends of micro RNAs anddozens of them participate in the regulation of cell death. Poor or impaired function of miRNAs and related disturbance in apoptotic signaling could lead to a number of pathological processes as tumorigenesis or disturbances in tissue development and homeostasis. . Understanding how miRNA functions in cell death and possible practical...
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Translational control in immune response.
Hlaváček, Adam ; Valášek, Leoš (advisor) ; Čáp, Michal (referee)
Immune reaction often requires a prompt modification of gene expression that in turn alters cellular physiology. There are an increasing number of articles supporting a critical role of translational control in this aspect of cellular biology. The aim of this work is to present some of cellular and molecular mechanisms that connect translational control and immune reaction in immune and somatic cells and can be possibly misused by some viruses. Perhaps not surprisingly, many immunologically relevant translational control mechanisms are similar to those acting during the stress response. Over the years it has been documented that the T cells, dendrocytes, Natural killer cells and macrophages utilize translational control for their immunological activation following stimulation. Combination of general and gene-specific translational control mechanisms enables fast changes in proteome and physiology that are characteristic for immune cell activation. The overall impact of translational control on immune response is further illustrated by the fact that it acts upon each stage of life of immune cells - from their activation, through survival, to a programmed cell death. Even in some non-immune cells the translational control plays an important role with respect to immunity, as these cells are known to have an...
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Molecular dynamics simulations of biomolecular complexes consisting of proteins and nucleic acids
Melcr, Josef ; Barvík, Ivan (advisor) ; Bok, Jiří (referee)
Literature search on the Elongation factor Tu (EF-Tu), which is involved in the process of translation of genetic information, was performed. Further, computational methods as molecular dynamics (MD) and Monte Carlo (MC) were studied. Then, computer programs for MD and MC simulations of a Lennard-Jones gas were developed. MD simulations were further applied to EF-Tu using the NAMD and ACEMD software packages. Multiprocessor PC clusters and programmable NVIDIA GPUs were used. MD simulations of EF-Tu uncovered binding of monovalent ions in nearby of the EF-Tu active site. The impact of Na$^+$ binding on evolutionarily conserved residues (His85, Val20, Ile61, Asp21, Tyr47, Asp87, etc.) was studied in detail.
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Impact of the rRNA modifications on protein synthesis
Kročová, Eliška ; Pospíšek, Martin (advisor) ; Holá, Dana (referee)
A ribosome is a supramolecular structure, which mediates synthesis of all cellular proteins, and therefore is essential for cell life. The fact, that some nucleotides of ribosomal RNA are modified, is known for forty years. However only recently, successful deeper studies on how the individual modifications are synthesized and what is their effect on ribosome synthesis and function appear. Some particular nucleotide modifications are important for the ribosome formation (like m1 acp3 Ψ1191 SSU), some others influence proper function of the ribosome (e.g. Um2921, Gm2922, Ψ2923 LSU, m1 acp3 Ψ1191 SSU). Majority of modified nucleotides in eukaryotic rRNA is being recognized by small nucleolar RNA (snoRNA). Few nucleotides is, however, recognized and subsequently modified by specific proteins. These proteins also play crucial role in ribosome maturation. In thesis presented, current knowledge on the role of ribosomal RNA nucleotide modifications during their formation and maturation, and on their function is summarized and overviewed.
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Internal ribosome entry site of the hepatitis C virus as a possible target for therapy
Roučová, Kristina ; Čáp, Michal (referee) ; Pospíšek, Martin (advisor)
Hepatitis C virus infects about 3 % of world's population. Progress in molecular biology and better knowledge of hepatitis C virus life cycle contribute to the development of specifically targeted antiviral therapies for HCV. This new treatment also targets the internal ribosome entry site (IRES), which is highly conserved and therefore an attractive target for intervention. In addition, inhibition of IRES function could disable the propagation of the virus early in the HCV life cycle. Novel therapeutics are aimed both at the HCV IRES structure and its nucleotide sequence. Small molecules and synthetic nucleic acids, e.g. antisense oligonucleotides and ribozymes, have been tested as potential therapeutic substances. In this paper particular attention is paid to small molecules interacting with HCV IRES.
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Algebra of dual quaternions in image analysis
Hrubý, Jan ; Návrat, Aleš (referee) ; Hrdina, Jaroslav (advisor)
This work has two goals. Firstly it is to acquaint the reader with the classical use of quaternions and dual quaternions in geometry. Secondly the generalization of the Fourier transform into the set of dual quaternions. At first it goes into algebraic properties and structure of quaternions and ways of their inscriptions. Later dual numbers are introduced and consecutively with their help dual quaternions. Then the work deals with description of rotations and translations using quaternions and dual quaternions, that enable their easy description. Finally the discreet dual quaternion Fourier transform is defined, and for its effective calculation the algorithm is derived, which is then brought into effect as a code in program environment MATLAB.
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Gene Searching - Web Application
Stiborová, Lucie ; Koutný, Jiří (referee) ; Burgetová, Ivana (advisor)
The aim of my Bachelor's Thesis is to create a user interface and to implement the web application with the genes' searching. This is the educational application when each user has a possibility of entering own nucleotide sequences or selecting a redefined chain. This application has to be able to read, process and decide on the existence of a potential gene. On the base of this simple statistic method the result is given back to the user.
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Web Application for Bioinformatics Education - Genetic Code
Kilián, Martin ; Martínek, Tomáš (referee) ; Burgetová, Ivana (advisor)
This thesis briefly describes basic informations in moleculary biology. Thesis deals with a transfer of information from DNA into RNA through uprotein, are also briefly described the methods and algorithms dealing with the detection of genome. The larger part deals with the recognition cue coded signals and determination of sequences and their subsequent transcription and translation, which demonstration program was needed to create. The final result is s web application as the education system.
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