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Recycling of spliceosomal complexes
Klimešová, Klára ; Staněk, David (advisor) ; Hálová, Martina (referee)
Most human genes are composed of coding sequences (exons) that are interrupted by non-coding sequences (introns). After gene transcription into pre-mRNA, these introns have to be removed in a process called splicing. Splicing is mediated by a very complex and dynamic complex called the spliceosome, which consists of five small nuclear ribonucleoprotein particles (snRNPs) and numerous additional splicing proteins. Each particle contains single small nuclear RNA and a set of specific proteins. SnRNPs are assembled by a stepwise process that takes place both in the nucleus and the cytoplasm and final maturation steps occur in nuclear Cajal bodies. The mature snRNPs interact with pre-mRNA in an ordered pathway and form the spliceosome that catalyzes two trans-esterification reactions leading to intron excision and exons ligation. Subsequently, the spliceosome disassembles again into individual snRNPs that have undergone diverse conformational and compositional transformations during splicing. Thus, before the particles can participate in another round of splicing they have to go through recycling to recover their original form. However, currently the recycling phase of the splicing cycle is surrounded by more questions than answers. The purpose of this work is to discuss latest findings that shed some light on...
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Role of microbiota and gut inflammation in the pathogenesis of experimental colorectal cancer
Klimešová, Klára ; Tlaskalová - Hogenová, Helena (advisor) ; Vítek, Libor (referee) ; Reiniš, Milan (referee)
Mucosal surface of the gut is in continuous contact with foreign compounds derived from diet as well as from commensal or pathogenic microorganisms. Thousands of years of symbiosis resulted in tight cooperation between the host and its microbiota. Microbiota composition and metabolism actively influence host's physiological as well as pathological processes. Chronic inflammation is characterized by prolonged active inflammatory response associated with tissue damage. This status results from accumulation of defects in various factors including gut barrier functions as well as mechanisms of innate and adaptive immunity. It's commonly accepted that chronic inflammatory diseases of the gastrointestinal tract like IBD, are associated with an increased risk of CAC development. Two publications related to this thesis deal with modulatory effects of peroral administration of components of commensal bacteria or probiotics on intestinal inflammation. Using acute or chronic model of DSS-induced colitis, we demonstrated that oral treatment of BALB/c mice with membranous fraction of the commensal, Parabacteroides distasonis, as well as with lysate of probiotic bacterium Lactobacillus casei DN-114 001 significantly reduces the severity of intestinal inflammation. Moreover, the treatment was associated with reduction of...
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Molecular mechanism of quality control during snRNP biogenesis
Klimešová, Klára ; Staněk, David (advisor) ; Krásný, Libor (referee) ; Vomastek, Tomáš (referee)
The spliceosome is one of the largest and most dynamic molecular machines in the cell. The central part of the complex is formed by five small nuclear ribonucleoproteins (snRNPs) which are generated in a multi-step biogenesis pathway. Moreover, the snRNPs undergo extensive rearrangements during the splicing and require reassembly after every intron removal. Both de novo assembly and post-splicing recycling of snRNPs are guided and facilitated by specific chaperones. Here, I reveal molecular details of function of two snRNP chaperones, SART3 and TSSC4. While TSSC4 is a previously uncharacterized protein, SART3 has been described before as a U6 snRNP-specific factor which assists in association of U6 and U4 particles into di-snRNP, and is important for the U4/U6 snRNP recycling. However, the mechanism of its function has been unclear. Here, I provide an evidence that SART3 interacts with a post-splicing complex and propose that SART3 could promote its disassembly. Our data further suggest that SART3 binds U6 snRNP already within the post-splicing complex and thus participates in the whole recycling phase of U6 snRNP. Then, I show that TSSC4 is a novel U5 snRNP-specific chaperone which promotes an assembly of U5 and U4/U6 snRNPs into a splicing-competent tri-snRNP particle. We identified...
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Zhodnocení současného stavu a péče o vybraná zvláště chráněná území okresu Žďár nad Sázavou
Klimešová, Klára
In this bachelor thesis has been evaluated 6 small-scale specially protected areas according to Methodology evalution of present state and management in small-scale specially protected areas (Svátek a Buček 2005). The total areas is 31,61 ha. Selected small-scale specially protected areas are located in district Žďár nad Sázavou. There are evaluated 2 nature reserves and 4 nature monuments. From results is implicit that present state is good in 1 nature reserve and in 3 nature monuments, and average for the remaining selected small-scale specially protected areas, which is 1 nature reserve and 1 nature monuments. Management is assessed at 5 small-scale specially protected areas as good and at 1 nature reserve as average. In the discussion has been compared with other results of evaluation small-scale specially protected areas in Czech Republic, which summarized Svátek (2012).
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Role of microbiota in mouse experimental model of psoriasis
Jirásková Zákostelská, Zuzana ; Stehlíková, Zuzana ; Klimešová, Klára ; Rossmann, Pavel ; Dvořák, Jiří ; Novosádová, Iva ; Kostovčík, Martin ; Coufal, Štěpán ; Šrůtková, Dagmar ; Hudcovic, Tomáš ; Štěpánková, Renata ; Rob, F. ; Jůzlová, P. ; Herzogová, J. ; Tlaskalová-Hogenová, Helena ; Kverka, Miloslav
Anotace v anglickém jazyce\n\nMouse model of human psoriasis and gnotobiotic are important tools in understanding the role of gut and skin microbiota in pathogenesis of psoriasis. In our experiments we showed that gnotobiotic mice, as well as conventional mice treated with antibiotics, have milder skin inflammation in comparison with control conventional mice. Treatment with broad spectrum antibiotics led to dramatic shift in gut microbial composition, in particular, we observed extensive increase of order Lactobacillales. To analyze the potential effect of Lactobacillales on skin inflammation, we further monocolonized mice with L. plantarum WCFS1. Also monocolonized mice showed lower skin inflammation in comparison with conventional mice. To understand whether microbial dysbiosis is cause or effect of psoriasis needs to be further investigated.\n\n
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The role of bacterium Escherichia coli in the tumorigenesis of colorectal carcinoma
Čurnová, Lenka ; Klimešová, Klára (advisor) ; Grobárová, Valéria (referee)
Colorectal carcinoma is a severe disease of colon. It belongs to the cancers with the highest incidence and also high mortality. In the process of tumorigenesis, there are applied various mechanisms, mainly DNA damage and subsequent reparation and inflammation. Gut microbiota plays an important role in development of the colorectal cancer influencing cancer microenvironment. Microbiota triggers inflammatory response or produces different toxins. The diploma thesis was aimed on the relation between the presence of cyclomodulin genes in the genome of individual strains of bacterium Escherichia coli and their genotoxic features. To follow direct influence of epithelial cells by microbiota, we used in vitro model. We chose E. coli as a model microorganism because it is common bacterium of human gut, moreover, as facultative anaerob it is easily cultivated. We used six strains of E. coli with different relation to the host organism including probiotic, comensal and pathobiont. In probiotic strains of E. coli (Nissle 1917 and O83), we detected less genes for cyclomodulins than in other strains. We did not observed significant differences in genotoxic features of the strains. Also, we did not detect any changes in viability, proliferation, activation of repair mechanisms or p53 fosforylation caused by...
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Mapping of SART3 interactions with spliceosomal snRNPs
Klimešová, Klára ; Staněk, David (advisor) ; Hnilicová, Jarmila (referee)
The splicing of pre-mRNA transcripts is catalyzed by a huge and dynamic machinery called spliceosome. The spliceosomal complex consists of five small nuclear ribonucleoprotein (snRNP) particles and hundreds of non-snRNP proteins. Biogenesis of spliceosomal snRNPs is a multi-step process, the final steps of which take place in a specialized sub-nuclear compartment, the Cajal body. However, molecular details of snRNP targeting to the Cajal body remain mostly unclear. Our previous results revealed that SART3 protein is important for accumulation of U4, U5 and U6 snRNPs in Cajal bodies, but how SART3 binds snRNP particles is elusive. SART3 has been identified as a U6 snRNP interaction partner and U4/U6 di-snRNP assembly factor. Here, we show that SART3 interacts with U2 snRNP as well, and that it binds specifically immature U2 particles. Next, we provide evidence that SART3 associates with U2 snRNP via Sm proteins, which are components of the stable snRNP core and are present in four out of five major snRNPs (i.e. in U1, U2, U4 and U5). We propose that the interaction between SART3 and Sm proteins represents a general SART3-snRNP binding mechanism, how SART3 recognizes immature snRNPs and quality controls the snRNP assembly process in Cajal bodies.
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Role of microbiota and gut inflammation in the pathogenesis of experimental colorectal cancer
Klimešová, Klára ; Tlaskalová - Hogenová, Helena (advisor) ; Vítek, Libor (referee) ; Reiniš, Milan (referee)
Mucosal surface of the gut is in continuous contact with foreign compounds derived from diet as well as from commensal or pathogenic microorganisms. Thousands of years of symbiosis resulted in tight cooperation between the host and its microbiota. Microbiota composition and metabolism actively influence host's physiological as well as pathological processes. Chronic inflammation is characterized by prolonged active inflammatory response associated with tissue damage. This status results from accumulation of defects in various factors including gut barrier functions as well as mechanisms of innate and adaptive immunity. It's commonly accepted that chronic inflammatory diseases of the gastrointestinal tract like IBD, are associated with an increased risk of CAC development. Two publications related to this thesis deal with modulatory effects of peroral administration of components of commensal bacteria or probiotics on intestinal inflammation. Using acute or chronic model of DSS-induced colitis, we demonstrated that oral treatment of BALB/c mice with membranous fraction of the commensal, Parabacteroides distasonis, as well as with lysate of probiotic bacterium Lactobacillus casei DN-114 001 significantly reduces the severity of intestinal inflammation. Moreover, the treatment was associated with reduction of...
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Recycling of spliceosomal complexes
Klimešová, Klára ; Staněk, David (advisor) ; Hálová, Martina (referee)
Most human genes are composed of coding sequences (exons) that are interrupted by non-coding sequences (introns). After gene transcription into pre-mRNA, these introns have to be removed in a process called splicing. Splicing is mediated by a very complex and dynamic complex called the spliceosome, which consists of five small nuclear ribonucleoprotein particles (snRNPs) and numerous additional splicing proteins. Each particle contains single small nuclear RNA and a set of specific proteins. SnRNPs are assembled by a stepwise process that takes place both in the nucleus and the cytoplasm and final maturation steps occur in nuclear Cajal bodies. The mature snRNPs interact with pre-mRNA in an ordered pathway and form the spliceosome that catalyzes two trans-esterification reactions leading to intron excision and exons ligation. Subsequently, the spliceosome disassembles again into individual snRNPs that have undergone diverse conformational and compositional transformations during splicing. Thus, before the particles can participate in another round of splicing they have to go through recycling to recover their original form. However, currently the recycling phase of the splicing cycle is surrounded by more questions than answers. The purpose of this work is to discuss latest findings that shed some light on...
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Gut microbiome and colorectal cancer
Tlaskalová-Hogenová, Helena ; Klimešová, Klára ; Zákostelská, Zuzana ; Kverka, Miloslav ; Hornová, Michaela ; Vannucci, Luca ; Štěpánková, Renata ; Hudcovic, Tomáš ; Kozáková, Hana ; Rossmann, Pavel
The work deals with metagenomic approaches that are currently being used to decipher the genome of the microbiota (microbiome), and, in parallel, functional studies are being performed to analyze the effects of microbiota on the host.
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