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Wireless transmission interference modeling (AWGN, Rayleigh, Rice fading channels)
Hloušek, Tomáš ; Gleissner, Filip (referee) ; Mikulka, Jan (advisor)
This thesis describes and models wirelesss transmission intereferences in real communication channels. A signal received on a fading channel is subjected to a multiplicative distortion and to the usual additive noise. Real channel adds to the signal noise and fadings. Gaussian noise is a result of channel awgn. Fadings is implicated by multipath propagation of signal in Rayleigh and Rician channels. Main goal of this project is to program BERsolve, which is created in tool GUIDE in Matlab. User program BERsolve makes it possible to analyse bit error rate and symbol error rate for some types of channel models, which are defined by standard COST207. BERsolve offers some other functions i.e. display time behaviour, constellation diagram and spectrum. This program provides us with an overview representation of problem by multipath interferences in communication channels.
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Functional study of the putative nucleotidase encoded by spr1057 gene in Streptococcus pneumoniae, a homologue of Escherichia coli protein YjjG
Vacková, Zuzana ; Branny, Pavel (advisor) ; Lichá, Irena (referee)
ANGLICKÝ ABSTRAKT Functional study of the putative nucleotidase encoded by spr1057 gene in Streptococcus pneumoniae, a likely homolog of Escherichia coli protein YjjG. Bacterial cells are constantly exposed to innumerable toxic substances, either in their external environment or by by-products of their own metabolism. For these reasons, the bacterial cells evolved several mechanisms to cope with this challenge. These mechanisms are represented by: blocking the uptake, export by specific transporters as well as specific inactivation of these substance by enzymes. A particular group of these toxic substances are noncanonica nucleotides, which can directly inhibit bacterial cell DNA replication or can result in increased mutation rate. Enzymes recognizing these modified derivatives are known as "house-cleaning" nucleotide phsphateses, which can inactivate the potentially mutagenic nucleotides and prevent their incorporation into DNA and RNA. Some of the "house- cleaning" enzymes belong to a group of haloacid dehalogenase enzymes (haloacid dehalogenase-like hydrolase superfamily), which are found in many bacterial species. This thesis is focused on the function of hypothetical protein Spr1057 of Streptococcus pneumoniae with an unknown function. Sequence comparison revealed that Spr1057 has a significant...
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Study of the unique signaling pathway of Ser/Thr protein kinase StkP and phosphatase PhpP in Streptococcus pneumoniae
Keil, Jan ; Ulrych, Aleš (advisor) ; Bobková, Šárka (referee)
The major human pathogen Streptococcus pneumoniae is a unique model for the study of eukaryotic-type serine/threonine protein kinases and its cognate phosphatases in bacteria, since it encodes only a single signaling pair composed of the StkP protein kinase and PhpP phosphatase. This signaling pair plays a role in several cellular processes, mainly in cell wall biosynthesis and cell division. StkP and PhpP proteins with a pleiotropic effect appear to regulate a complex signaling cascade by phosphorylation of many substrates. However, only a few have been characterized so far. Using MS analysis, we have identified about 90 phosphopeptides that are potential substrates for the StkP kinase and PhpP phosphatase. This diploma thesis is focused on the characterization of the new substrate Spr0929 and its role in pneumococcal physiology. One of the objectives was to investigate cell morphology of strains carrying deletion of the spr0929 gene in different genetic backgrounds. It turned out that the role of Spr0929 in cell morphology is strain specific. The growth curves of strains with this deletion were compared to that of the wild type in various physiological conditions as well. As Spr0929 contains a nucleoid-associated domain called NdpA, determination of its cell localization was an important...
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Ser/Thr protein kinases in mycobacteria
Borovcová, Taťána ; Doubravová, Linda (advisor) ; Konopásek, Ivo (referee)
The Mycobacterium tuberculosis genome encodes 11 Ser/Thr protein kinases. These protein kinases are structurally related to eukaryotic protein kinases. The phosphoproteome contains hundreds of proteins phosphorylated on Ser/Thr residues that influence all aspects of cell biology, which supports the critical role of phosphorylation in the regulation of physiology. Particularly important role in regulation belongs to protein kinases PknA, PknB, PknG and PknL, these protein kinases occur in all species of mycobacteria. Although only PknA and PknB are essencial for the M. tuberculosis, they regulate cell shape through the regulation of cell wall synthesis and cell division. Another important protein kinase is PknG, although not essential for growth it is necessary for virulence, because it promotes the survival of pathogen inside macrophages of the host. As a result, Ser/Thr protein kinases represent an interesting target for inhibitor development that could be used as drugs against tuberculosis.
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Significance of protein phosphorylation for bacterial cell
Gregorová, Michaela ; Branny, Pavel (advisor) ; Lišková, Petra (referee)
Phosphorylation - most common post-translational modification has an important role in many cellular processes of bacteria. Bacteria contain enzymes that are in charge of adding phosphoryl group (kinases) or enzymes with reciprocal activity (phosphatases). Reversible phosphorylation and dephosphorylation of proteins are fundamental for signal transduction from the environment to the cell. These modifications can affect enzymatic activity, protein stability, localization as well as interaction with another protein. Due to the complexity of these phosphorylation networks, bacterial cells are capable to adapt very effectively to changing environmental conditions.
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The role of protein kinase StkP in regulation of the cell division in Streptococcus pneumoniae
Malíková, Eliška ; Doubravová, Linda (advisor) ; Kuthan, Martin (referee)
Protein phosphorylation by protein kinases is a key mechanizm that enables both eukaryotic and prokaryotic organizm sense and read environmental signals and convert these signals into changes in gene expression and thus proper biological response. One of the main phosphorylation systems in bacteria consists of eukaryotic-like Ser/ Thr protein kinases. The genome of human pathogen Streptococcus pneumoniae contains single Ser/ Thr protein kinase StkP. StkP regulates virulence, competence, stress resistance, gene expression and plays an important role in the regulation of cell division cycle. Analysis of phosphoproteome maps of both wild type and ΔstkP mutant strain of S. pneumoniae showed that in vivo StkP phosphorylates several putative substrates including the cell division protein DivIVA (NOVÁKOVÁ et al., 2010). DivIVA in S. pneumoniae is localized at midcell and at the cell poles. It was proposed to be primarily involved in the formation and maturation of the cell poles (FADDA et al., 2007). The aim of this thesis was to investigate phosphorylation of the cell division protein DivIVA in S. pneumoniae. Gene divIVA was cloned, expressed in E. coli and protein was purified via affinity chromatography. Phosphorylation of DivIVA by StkP was examined in a kinase assay. We confirmed that DivIVA is a direct...
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Functional studies of Ser/Thr protein kinases and phosphatases of Pseudomonas aeruginosa
Goldová, Jana ; Branny, Pavel (advisor) ; Nešvera, Jan (referee) ; Španová, Alena (referee)
Reversible protein phosphorylation is considered the universal language for intracellular communication in all living organisms. This process, catalysed by protein kinases and phosphatases, enables the translation of extracellular signals into cellular responses and also allows for adaptation to a constantly changing environment. In recent years, a number of bacterial eukaryotic-type Ser/Thr protein kinases and phosphatases have been identified. However, their precise functions and substrates are not yet well defined. The genome of opportunistic human pathogen Pseudomonas aeruginosa contains at least five genes encoding putative eukaryotic-type Ser/Thr protein kinases and phosphatases. In the first part of this study, we have attempted to establish the role of Ser/Thr protein kinase PpkA and phosphatase PppA, which belong to type VI secretion system H1-T6SS. Double mutant strain ∆pppA-ppkA was prepared in P. aeruginosa PAO1 background. Phenotypic studies revealed that the mutant grew slower than the wild-type strain in minimal media and exhibited reduced secretion of pigment pyocyanin. In addition, the mutant had altered sensitivity to oxidative and hyperosmotic stress conditions. Consequently, mutant cells had an impaired ability to survive in murine macrophages and an attenuated virulence in the...
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Functional study of the putative nucleotidase encoded by spr1057 gene in Streptococcus pneumoniae, a homologue of Escherichia coli protein YjjG
Vacková, Zuzana ; Lichá, Irena (referee) ; Branny, Pavel (advisor)
ANGLICKÝ ABSTRAKT Functional study of the putative nucleotidase encoded by spr1057 gene in Streptococcus pneumoniae, a likely homolog of Escherichia coli protein YjjG. Bacterial cells are constantly exposed to innumerable toxic substances, either in their external environment or by by-products of their own metabolism. For these reasons, the bacterial cells evolved several mechanisms to cope with this challenge. These mechanisms are represented by: blocking the uptake, export by specific transporters as well as specific inactivation of these substance by enzymes. A particular group of these toxic substances are noncanonica nucleotides, which can directly inhibit bacterial cell DNA replication or can result in increased mutation rate. Enzymes recognizing these modified derivatives are known as "house-cleaning" nucleotide phsphateses, which can inactivate the potentially mutagenic nucleotides and prevent their incorporation into DNA and RNA. Some of the "house- cleaning" enzymes belong to a group of haloacid dehalogenase enzymes (haloacid dehalogenase-like hydrolase superfamily), which are found in many bacterial species. This thesis is focused on the function of hypothetical protein Spr1057 of Streptococcus pneumoniae with an unknown function. Sequence comparison revealed that Spr1057 has a significant...
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Wireless transmission interference modeling (AWGN, Rayleigh, Rice fading channels)
Hloušek, Tomáš ; Gleissner, Filip (referee) ; Mikulka, Jan (advisor)
This thesis describes and models wirelesss transmission intereferences in real communication channels. A signal received on a fading channel is subjected to a multiplicative distortion and to the usual additive noise. Real channel adds to the signal noise and fadings. Gaussian noise is a result of channel awgn. Fadings is implicated by multipath propagation of signal in Rayleigh and Rician channels. Main goal of this project is to program BERsolve, which is created in tool GUIDE in Matlab. User program BERsolve makes it possible to analyse bit error rate and symbol error rate for some types of channel models, which are defined by standard COST207. BERsolve offers some other functions i.e. display time behaviour, constellation diagram and spectrum. This program provides us with an overview representation of problem by multipath interferences in communication channels.
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