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On-Line Monitoring of Expiration of DNSSEC Signatures
Mrázek, Jakub ; Polčák, Libor (referee) ; Matoušek, Petr (advisor)
In the bachelor thesis we have described computer software (programme) which is supposed to check the signatures of DNS (Domain Name System) records (resource records) and warn in due time about the expiry date or the approaching expiry date of the signatures in order to prevent from expiring. In the paper we have specified the DNSSEC (Domain Name System Security) technology, new resource records for the DNSSEC and details of signing the resource records. Moreover, we have introduced the programme itself, the possibilities of setting the programme, the ways of data reading and warning output. Since no such programme exists, and because there is a need to check the signatures quickly and warn about their expiry date, we have decided for this work.
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Modelling of OSPFv3 Link-State Routing Protocol
Mrázek, Jakub ; Grégr, Matěj (referee) ; Veselý, Vladimír (advisor)
OMNeT++ is a discrete event, modular simulator often used for simulation of computer networks. The universal simulator can be extended by various packages, such as INET framework, which is used for simulation of devices and TCP/IP protocols. This thesis examines facilities of INET package in the routing that is dynamic routing protocols. Concretely, it aims at OSPF protocol for IPv6 networks (OSPFv3). The protocol is presented and its principles are interpreted. The work is designed to simulate the module OSPFv3 protocol and module is partially implemented.
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Změny střevního mikrobiomu u pacietů s idiotypickými střevními záněty léčenými pomocí anti-TNF-α
Damašková, Dagmar ; Mrázek, Jakub (advisor) ; Drbal, Karel (referee)
English Abstract Crohn's disease together with ulcerative colitis, is a type of inflammatory bowel disease (IBD) with increasing incidence and prevalence in developed countries. IBD is an immunologically mediated multifactorial disease and it's mechanism of action is still unknown. Current well- established treatment targets the inflammation with corticosteroids and immunosuppressive drugs. Apart from the intestinal inflammation, which is the primary target of the treatment, patients are characteristically afflicted with intestinal dysbiosis. Therefore, possible interventions might be an adjuvant or biological therapy. Adjuvant therapy directly aims the microbiota with probiotics, whereas the target of biological therapy is TNF-α, a pro- inflammatory cytokine excessively secreted by macrophages. The aim of this thesis is to evaluate intestinal microbiota composition changes in IBD patients with regard to courses of adjuvant and biological therapy. Bacterial diversity was analyzed using three different DNA extraction techniques. Rapid beat beating + column (RBB+C) was chosen for analyzing patient samples, as it showed the highest DNA yield and the highest DNA purity. Primarily the bacterial diversity was analyzed using degradation gradient gel electrophoresis (DGGE) with subsequent sequencing of bands of...
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Ecological aspects affecting microbiota in the digestive tracts of birds
Schmiedová, Lucie ; Kreisinger, Jakub (advisor) ; Mrázek, Jakub (referee) ; Gvoždíková Javůrková, Veronika (referee)
The results indicate that songbird GM is dominated by the bacterial phyla Proteobacteria, Firmicutes, Actinobacteria, Tenericutes, Bacteroidetes and Chlamydia, a community that differs from that of mammals. A t the interspecies l evel, GM composition is mainly influenced by phylogeny and less so by sampling site. While ecological factors , and especially diet , are important GM predictors in mammals, the effect of ecological factors , including diet , have a much smaller effect on inte r - and intraspecific variability in songbird GM composition . Our data from barn swallows ( Hirundo rustica ) suggest an effect of social GM transmission among adults forming social pair s, as well as trans - generational transmission from a social mother to her own nestlings. At the same time, we observed differ ing GM in adults and nestlings, with no dramatic change in GM with nestling age, a process previously recognised in mammals. Part of the GM detected appears to remain stable over time , and is therefore su itable for further detailed study. To conclude, our studies demonstrate that s ongbird GM differs from that of mammals and that the factors influencing GM composition appear to differ from those in mammals , thereby highlighting the importance of study ing mu ltiple vertebrate groups (not just mammals ) when...
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Changes in microbial colonization of gastrointestinal tract in patients after allogeneic hematopoietic stem cell transplantation
Michková, Petra ; Mrázek, Jakub (advisor) ; Kodešová, Tereza (referee)
Introduction: Physiological microflora is characterised by wide diversity. The microbial community is mostly composed of bacteria, but also includes fungi, archaea and viruses. Anaerobic commensal bacteria (Firmicutes and Bacteroidetes) dominate 90% of the colon. The composition and products of the gut microbiota have a significant effect on an individual's immune system, and their interactions may ultimately promote immune tolerance or inflammatory immune response. Blood cell transplantation (HSCT) and its associated standard procedures of conditioning, antibiotic exposure and dietary prophylaxis represent modification and disruption of the gut microbiota leading to the development of some serious post-transplant complications affecting the OS (overall survival) and TRM (treatment related mortality) of patients. Objectives: The aim of this work was to investigate the representation of individual bacterial strains in patients undergoing allogeneic HSCT, as well as the effect of transplantation on the composition and diversity of their gut microbiota. Methods: Stool samples were obtained from 52 patients who underwent an allogeneic hematopoietic cell transplant at the Institute of Hematology and Blood Transfusion in Prague. A cut-off date for the first sample was set for the start of...
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Bacteriophage 936 by qPCR quantification in dairy products.
Olša Fliegerová, Kateřina ; Mrázek, Jakub ; Štrosová, Lenka ; Němečková, I. ; Kopečný, Jan
Virulent bacteriophages are still representing significant threat in dairy production even with frequent disinfection and sterilization all the equipment in dairy plants. Therefore a reliable \nmethod of phage monitoring and quantification necessary part of phage prevention. Method is based on qPCR amplification and fluorescent detection of copies number of the phage main\nstructural protein and therefore is independent on the phage cultivation. It is quick, reliable a sensitive enough to estimate phage copy numbers in dairy starters and whey in any phase of dairy production. \n
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Study of culturable anaerobic bacterial communities living in symbiosis with bark beetles; its isolation, taxonomy and biotechnical potential.
Fabryová, Anna ; Garcia-Fraile, Paula (advisor) ; Mrázek, Jakub (referee)
Microbial enzymes implicated in plant cell hydrolysis may have several potential aplications such as biomass degradation biocatalysts or with biofuel production. Bark beetles establish symbiosis with several microbial strains which play different roles benifitting the beetle, as the production of hydrolytic enzymes to degrade the ingested wood, the protection against mirobial antagonist or the detoxification of the environment. Fungal symbionts have been traditionally the best studied, but several recent research with bacterial symbionts of several bark beetle species show that bacterial also display important functions for the host. In this study, the bacterial communities of the bark beetle species Cryphalus piceae and Pithophtorus pithophtorus, collected in the Czech Republic from pine and fir trees, respectively, were isolated and 55 out of 89 samples were identified by 16S rRNA gene amplification and sequencing. Members of the genera Erwinia, Pantoea, Curtobacterium, Yersinia, Pseudomonas and Staphylococcus were detected. The isolates were object of study for their possible biotechnological potential in (ligno)cellulose materials degradation by screening several enzymes implicated in plant cell hydrolysis, as cellulases, xylanases, amylases, laccases, as well as their capability for colorant...
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Změny střevního mikrobiomu u pacietů s idiotypickými střevními záněty léčenými pomocí anti-TNF-α
Damašková, Dagmar ; Mrázek, Jakub (advisor) ; Drbal, Karel (referee)
English Abstract Crohn's disease together with ulcerative colitis, is a type of inflammatory bowel disease (IBD) with increasing incidence and prevalence in developed countries. IBD is an immunologically mediated multifactorial disease and it's mechanism of action is still unknown. Current well- established treatment targets the inflammation with corticosteroids and immunosuppressive drugs. Apart from the intestinal inflammation, which is the primary target of the treatment, patients are characteristically afflicted with intestinal dysbiosis. Therefore, possible interventions might be an adjuvant or biological therapy. Adjuvant therapy directly aims the microbiota with probiotics, whereas the target of biological therapy is TNF-α, a pro- inflammatory cytokine excessively secreted by macrophages. The aim of this thesis is to evaluate intestinal microbiota composition changes in IBD patients with regard to courses of adjuvant and biological therapy. Bacterial diversity was analyzed using three different DNA extraction techniques. Rapid beat beating + column (RBB+C) was chosen for analyzing patient samples, as it showed the highest DNA yield and the highest DNA purity. Primarily the bacterial diversity was analyzed using degradation gradient gel electrophoresis (DGGE) with subsequent sequencing of bands of...
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On-Line Monitoring of Expiration of DNSSEC Signatures
Mrázek, Jakub ; Polčák, Libor (referee) ; Matoušek, Petr (advisor)
In the bachelor thesis we have described computer software (programme) which is supposed to check the signatures of DNS (Domain Name System) records (resource records) and warn in due time about the expiry date or the approaching expiry date of the signatures in order to prevent from expiring. In the paper we have specified the DNSSEC (Domain Name System Security) technology, new resource records for the DNSSEC and details of signing the resource records. Moreover, we have introduced the programme itself, the possibilities of setting the programme, the ways of data reading and warning output. Since no such programme exists, and because there is a need to check the signatures quickly and warn about their expiry date, we have decided for this work.
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