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Antimicrobial peptides inhibiting DNA synthesis.
Michková, Sára ; Krásný, Libor (advisor) ; Rejman, Dominik (referee)
Antimicrobial peptides (AMPs) are short amino acid sequences synthesized by a spectrum of organisms as a defence mechanism against bacteria. AMPs are divided into two groups based on their mechanisms of action - membrane disruptive AMPs and AMPs with an intracellular target. Bacteria themselves can also produce these toxins that help them compete with other strains within the same ecological niche. One such a peptide is sublancin - an AMP secreted by the soil bacterium Bacillus subtilis. Sublancin is bactericidal against Gram-positive bacteria. Although the exact mechanism of action of sublancin against bacteria is not yet well understood, it is known to target intracellular processes. It was proposed that sublancin could have a negative impact on DNA replication. This bachelor thesis first provides a brief description of DNA replication and then summarizes current knowledge about AMPs that target membrane and AMPs with intracellular targets. Detailed attention is then focused on AMPs that affect nucleic acid synthesis, a mechanism also proposed for sublancin. The final part of this work describes sublancin - its expression, structure, and possible mechanism(s) of action. Key words: antimicrobial peptide, interspecies competition, sublancin, Bacillus subtilis, DNA replication
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Emergent properties of the G1/S network
Dražková, Jana ; Tomášek, Petr (referee) ; Palumbo,, Pasquale (advisor)
Tato práce se zabývá buněčným cyklem kvasinky Saccgaromyces cerevisiae. Oblastí našeho zájmu je přechod mezi G1 a S fází, kde je naším cílem identifikovat velikosti buňky v době počátku DNA replikace. Nejprve se věnujeme nedávno publikovanému matematickému modelu, který popisuje mechanismy vedoucí k S fázi. Práce poskytuje detailní popis tohoto modelu, stejně jako časový průběh některých důležitých proteinů či jejich sloučenin. Dále se zabýváme pravděpodobnostním modelem aktivace replikačních počátků DNA. Nově uvažujeme vliv šíření DNA replikace mezi sousedícími počátky a analyzujeme jeho důsledky. Poskytujeme také senzitivní analýzu kritické velikosti buňky vzhledem ke konstantám popisujícím dynamiku reakcí v modelu G1/S přechodu.
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Biogenesis and function of nuclear iron-sulfur proteins
Panova, Ekaterina ; Benda, Martin (advisor) ; Smutná, Tamara (referee)
Iron-sulfur clusters are important inorganic cofactors of many cellular reactions, including those that occur in the nucleus. Nuclear iron-sulfur proteins play an important role in DNA replication, genome repair, and maintenance of genome stability. The biosynthesis of these iron-sulfur clusters is initiated in the mitochondria by the iron-sulfur cluster assembly pathway (ISC), continues in the cytosol by the cytosolic iron-sulfur cluster assembly pathway (CIA), and ends with the incorporation of the clusters into target apoproteins such as polymerases, primases, helicases, endonucleases, or glycosylases. This bachelor thesis summarizes current knowledge about the pathways of iron-sulfur cluster biosynthesis, the functions of nuclear iron-sulfur proteins, and the role of the clusters in these proteins, including the phenotypes and clinical manifestations caused by the absence of iron-sulfur clusters. Keywords: iron-sulfur clusters, metalloproteins, nucleus, DNA replication, DNA repair
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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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Structure-function organization of the cell nucleus.Microscopical analysis of nuclear subcompartments.
Jůda, Pavel ; Cmarko, Dušan (advisor) ; Mokrý, Jaroslav (referee) ; Kučera, Tomáš (referee) ; Smetana, Karel (referee)
Pavel Jůda - Abstract The cell nucleus is a complex cellular organelle. The nucleus and nuclear processes are organized into functionally and morphologically separated nuclear subcompartments. This thesis is particularly concerned with the three following nuclear subcompartments: sites of DNA replication, Polycomb bodies and nuclear inclusions constituted of inosine monophosphate dehydrogenase 2 (IMPDH2). First, we examined the relationship between MCM proteins and DNA replication. Using immunofluorescent labeling of cells extracted prior fixation and applying cross-correlation function analysis, we showed that MCM proteins are present at the sites of active DNA synthesis. Our results contributed to the solving of the first part of so-called MCM paradox. Second, we studied the structural basis of the Polycomb bodies. Based on fluorescence microscopy studies, Polycomb bodies have been considered to be the nuclear subcompartments formed by the accumulation of Polycomb proteins in the interchromatin compartment. In our work, using correlative light electron microscopy and experimental changes in macromolecular crowding, we clearly showed that a Polycomb body is a chromosomal domain formed by an accumulation of heterochromatin structures, rather than a typical nucleoplasmic body. Third, we were interested in...
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Structure-function organization of the cell nucleus.Microscopical analysis of nuclear subcompartments.
Jůda, Pavel ; Cmarko, Dušan (advisor) ; Mokrý, Jaroslav (referee) ; Kučera, Tomáš (referee) ; Smetana, Karel (referee)
Pavel Jůda - Abstract The cell nucleus is a complex cellular organelle. The nucleus and nuclear processes are organized into functionally and morphologically separated nuclear subcompartments. This thesis is particularly concerned with the three following nuclear subcompartments: sites of DNA replication, Polycomb bodies and nuclear inclusions constituted of inosine monophosphate dehydrogenase 2 (IMPDH2). First, we examined the relationship between MCM proteins and DNA replication. Using immunofluorescent labeling of cells extracted prior fixation and applying cross-correlation function analysis, we showed that MCM proteins are present at the sites of active DNA synthesis. Our results contributed to the solving of the first part of so-called MCM paradox. Second, we studied the structural basis of the Polycomb bodies. Based on fluorescence microscopy studies, Polycomb bodies have been considered to be the nuclear subcompartments formed by the accumulation of Polycomb proteins in the interchromatin compartment. In our work, using correlative light electron microscopy and experimental changes in macromolecular crowding, we clearly showed that a Polycomb body is a chromosomal domain formed by an accumulation of heterochromatin structures, rather than a typical nucleoplasmic body. Third, we were interested in...
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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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Emergent properties of the G1/S network
Dražková, Jana ; Tomášek, Petr (referee) ; Palumbo,, Pasquale (advisor)
Tato práce se zabývá buněčným cyklem kvasinky Saccgaromyces cerevisiae. Oblastí našeho zájmu je přechod mezi G1 a S fází, kde je naším cílem identifikovat velikosti buňky v době počátku DNA replikace. Nejprve se věnujeme nedávno publikovanému matematickému modelu, který popisuje mechanismy vedoucí k S fázi. Práce poskytuje detailní popis tohoto modelu, stejně jako časový průběh některých důležitých proteinů či jejich sloučenin. Dále se zabýváme pravděpodobnostním modelem aktivace replikačních počátků DNA. Nově uvažujeme vliv šíření DNA replikace mezi sousedícími počátky a analyzujeme jeho důsledky. Poskytujeme také senzitivní analýzu kritické velikosti buňky vzhledem ke konstantám popisujícím dynamiku reakcí v modelu G1/S přechodu.
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