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DNA topology as a factor affecting transcription in bacteria
Hladíková, Kristýna ; Krásný, Libor (advisor) ; Nešvera, Jan (referee)
DNA topology plays a key role in regulation of gene expression by affecting interactions between DNA and RNA polymerase and other regulatory proteins. In this work, I review the process of transcription and selected mechanisms of its regulation, focusing on the effects of DNA topology. A key characteristic of DNA topology is the level of supercoiling. I describe how the DNA supercoiling influences initiation of transcription, and how it is affected by topoisomerases and nucleoid-associating proteins. I then discuss selected examples of regulation of gene expression by topology. Finally, I discuss the alternative σN factor from Bacillus subtilis, which allows more efficient transcription initiation from linear (i.e. relaxed) rather than supercoiled DNA templates. In this property, σN diametrically differs from other σ factors. Key words: DNA, topology, RNA polymerase, transcription, promoter, sigma factor
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Regulation of transcription in Streptococcus pneumoniae
Zajíčková, Adéla ; Doubravová, Linda (advisor) ; Hnilicová, Jarmila (referee)
Regulation of transcription in Streptococcus pneumoniae Streptococcus pneumoniae, an opportunistic human pathogen, encodes a single eukaryotic-like Ser/Thr kinase, StkP, which plays a crucial role in cell growth and division. In a phosphoproteomic study, StkP-dependent phosphorylation of SigAunder antibiotic- induced stress conditions was demonstrated in vivo. SigA, a housekeeping factor, in complex with RNA polymerase, is responsible for the transcription of most genes in S. pneumoniae. Therefore, phosphorylation of this important regulator might play an important role in transcriptional regulation. In this work, we confirmed that StkP phosphorylates SigA at residues T291 and T306 in vitro. However, we could not detect SigA phosphorylation in vivo, and the role of phosphorylation remains to be elucidated. We detected all RNAP subunits, including SigA, in the RNAP complex of S. pneumoniae by mass spectrometry analysis. The protein Spr0726 was identified as part of the RNAP complex. The reciprocal interaction between Spr0726 and RNAP was confirmed by immunoprecipitation experiments. In functional studies, we found that deletion of the spr0726 gene leads to a decrease in the amount of the subunits β and α in the RNAP complex. Our data suggest that the Spr0726 protein may affect the stability of the RNAP...
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Slovak National Uprising
Orság, Michal ; Terén, Laco (referee) ; Ambrůz, Jan (advisor)
The aim of the thesis was to bring events after 1945, when there was a period of remembrance in the company , which served as a therapy , politics and aesthetics . Work on the memories gradually morphed into , among other things , to the monuments that act against collective oblivion . Arise place of remembrance , which relate to historical events and private stories . Partisan monuments fill in the country which they have to remind essentially absent . Again remembering you and gets to the surface again forgotten information that creating a logical connection form the structure . This structure is subject to change , which helped by rewriting and overlapping information in different layers of the structure . Neither art does not avoid the remembrance and forgetting , and creates a theme of a strategy , which is included rewriting . Media and individual override blank sheets in the past, currently , collecting and composing the mosaic , which allows you to create your own identity.
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Fourier transformation for exon prediction
Rusina, Michal ; Škutková, Helena (referee) ; Maděránková, Denisa (advisor)
In this bachelor thesis there are described the methods of the prediction of exon. The first part is aimed at the difference between the prokaryotic and eukaryotic organisms, the description of the DNA structure and the explanation of the terms exon and intron. The second section of the theoretic part includes four methods of the prediction of exons namely dynamic programming, neural networks, hidden Markov models and discrete Fourier transform. In the practical part there was created the program called Predikce_exonu that searches exons in nucleotide sequences and works on the principle of the Fourier transform. This algorithm together with 3 freely available programs was tested on 25 sequences and the success of their prediction was described by sensitivity and specificity.
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Comparison of Accuracy of Siri, Cortana and Google
Procingerová, Lucie ; Černocký, Jan (referee) ; Szőke, Igor (advisor)
The aim of this thesis is to compare the accuracy of translation of spoken word into text using several services. Primary it is about applications from Apple Inc., Microsoft Corporation and Google Inc., but there is also included several others, mostly available on-line. This document contains a descriptionn of the problem, analyzes the progress for each service. Subsequently, the test results are analyzed and compared with the reference outputs. In conclusion, there is a discussion of these experiments.
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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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The Technology of Subtitles in Films and other Media
Tobiášová, Eliška ; Jašková, Jana (referee) ; Froehling, Kenneth (advisor)
Účelem bakalářské práce je prozkoumat technologii titulkování. Ta je rozebrána historického, současného a budoucího hlediska. V práci jsou zmíněny i specifické způsoby využití titulků pro určité typy médií a součástí je i rozbor cílových skupin, pro které jsou titulky určeny. Kromě teoretického rozboru technologie titulkování je na závěr proveden experiment, jehož účelem je porovnat přesnost titulkování mezi strojově generovanými titulky, profesionální prací a amatérskou prací. Toho je dosaženo porovnáváním titulků ze stejných filmových scén vedle sebe v tabulkách. Výsledek výzkumu, který je odvozen na základě kritérií, zmíněných v práci, ukazuje, že profesionální titulky jsou nejspolehlivější cestou.
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Topic Identification from Spoken TED-Talks
Vašš, Adam ; Ondel, Lucas Antoine Francois (referee) ; Kesiraju, Santosh (advisor)
Táto práca sa zaoberá problémom spracovania prirodzeného jazyka a následnej klasifikácie. Použité systémy boli modelované na TED-LIUM korpuse. Systém automatického spracovania jazyka bol modelovaný s použitím sady nástrojov Kaldi. Vo výsledku bol dosiahnutý WER s hodnotou 16.6%. Problém klasifikácie textu bol adresovaný s pomocou metód na lineárnu klasifikáciu, konkrétne Multinomial Naive Bayes a Linear Support Vector Machines, kde druhá technika dosiahla vyššiu presnosť klasifikácie.
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