|
|
Nucleotide density for finding CpG islands
Sikorová, Eva ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with searching for CpG islands in the DNA sequences using the nucleotide density vectors. The first part includes view of the DNA structure, the genetic information expression, more detailed analysis of CpG islands and primarily their detection methods. In the practical part the algorithm for graphical representation of nucleotides on the basis of their densities and detections of CpG islands of artificially created and real DNA sequences was realized in the MATLAB program. The thesis includes the analysis of twenty sequences with the expected content of CpGIs and the comparison of results between the created program and two search engines.
|
|
|
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.
|
|
|
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.
|
|
|
Prediction of Quadruplex Structure
Mikula, Adrian ; Lexa, Matej (referee) ; Martínek, Tomáš (advisor)
This master's thesis focuses on search and structure prediction of quadruplexes in DNA sequences. Thesis also explains related terms that are important for understanding the function, properties and geometry of quadruplexes. Thesis describe physico-chemical and computational current methods, which possible to discover and structure prediction. This paper also explain the principle of molecular modelling, which was used in the final application. Design and implementation of the final algorithm are also part of this thesis.
|
|
|
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.
|
|
|
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.
|
|
|
Tolerance of DNA damage by novel biologically active platinum complexes
Vystrčilová, Jana ; Vrána, Oldřich (referee) ; Nováková,, Olga (advisor)
The anti-tumor activity of platinum based drugs is mediated by their ability to attack DNA. Platinum complexes can alter the structure of DNA by modifying the bases, mainly guanines. The biological consequnces of such interactions are compromising replication and transcription. RNA polymerase complex can stall at a damaged site in DNA and mark the lesion for repair by proteins that are utilized to execute nucleotide excision repair, a pathway commonly associated with the removal of bulky DNA damage from the genome. This RNA polymerase-induced repair pathway is called transcription-coupled nucleotide excision repair. Main goal of this thesis was to study RNA polymerases tolerance of DNA damage by novel, biologically active platinum (II) complexes involving derivatives of aromatic cytokinines as the ligands; cis-[Pt(2-chloro-6-(4-methoxybenzylamino)-9-isopropylpurin)2Cl2](PR-001), cis-[Pt(2-chloro-6-(benzylamino)-9-isopropylpurin)2Cl2](PR-002 )and cis-[Pt(2-(3-hydroxypropylamino)-6-(benzylamino)-9-isopropylpurin)2Cl2](PR-005). DNA templates (constructs) that contain a single, site-specific DNA lesion and support transcription by human RNA polymerase II and bacteriophage T7 RNA polymerase were prepared. The method is making use of polymerase chain reaction (PCR) and biotin-streptavidin interactions and paramagnetic particles to purify the final product. Synthetic oligomers duplexes (75-mer, 56-mer and 15-mer) are ligated to 5´-biotin pCI-neo-G-lessT7 PCR fragment, the 15-mer is either unmodified or modified with a site-specific lesion of PR-005 and cisplatin. We also studied the inhibition of RNA polymerases activity on globally modified plasmid pCI-neo and pUC 19 by novel platinum complexes and cisplatin. We found that bifunctional adducts of complex PR-005 contrary to adducts of PR-001 and PR-002 effectively decrease amount of full lenght transcripts produced by both, human and bacterial RNA polymerases. This result can be explained by a sterical block, induced to DNA by intrastrand cross-link of PR-005 with bulky aromatic ligands.
|
|
| |
|
|
Cold adaptation of insects: the role of shock proteins from Hsp family.
ŠTĚTINA, Tomáš
Heat shock proteins (Hsps) form evolutionarily conserved group of proteins that are best known for their unique function in repair of miss folded proteins that would otherwise aggregate in cells during stress conditions. The most extensively studied is the inducible Hsp70. Using 3rd instar larvae of transgene mutant of fruit fly, Drosophila melanogaster that lacks all copies of hsp70 gene, we assessed: 1) whether the absence of this gene is deleterious for larvae in their capacity to survive cold stress; and 2) whether any other gene from Hsps family may compensate for the loss of hsp70. We found that 1) survival of cold stress is not altered in Hsp- larvae when compared to wild type Hsp+ larvae; 2) there is no other gene of Hsps family that would compensate for the loss of hsp70 at the level of transcription. Our ongoing effort is focusing on analysis of cold stress response at the protein level.
|
|
|
Structural and functional characterization of giant plant Ogre-like retrotransposons
STEINBAUEROVÁ, Veronika
Ogre elements represent a distinct group of Ty3/gypsy LTR retrotransposons occurring in a range of dicot plants. They are characterized by two specific features ? presence of long extra open reading frame in 5´ untranslated region with unknown function and a non-coding sequence containing several stop codons separating protease and reverse transcriptase domains which was proposed to be removed by splicing. This thesis describes the functional analysis of intron splicing in Ogre retrotransposons. Further, it investigates additional coding information not only in Ogre retrotransposons but in the whole group of Ty3/gypsy retroelements.
|
guest ::
