National Repository of Grey Literature 301 records found  1 - 10nextend  jump to record: Search took 0.00 seconds. 
Jumping Language Models
Ošmera, Lubomír ; Kocman, Radim (referee) ; Meduna, Alexandr (advisor)
The main goal of this master thesis is introduction and investigation of extended version of jumping automata and grammars. New versions are primarily focused on bioinformatic applications - DNA computing. This thesis examine their power and other properties of new models and makes comparison with existing computer science models. Then thesis demontrates practical applications, specifically amino acid and protein detections inside DNA sequence and makes comparision with existing tools in DNA computing for example Mark´s probabilistic models.
Implementation of local DNA structures analysis tool
Kaura, Patrik ; Trenz, Oldřich (referee) ; Šťastný, Jiří (advisor)
This diploma thesis is focused on the description and implementation of the API wrapper application, which works on top of computational core ibp bioinformatics. The first half of the thesis is focused on the summary of basic knowledge in the field of DNA research, as well as the specification of the problem and description of selected technologies. The other half deals with the actual implementation, distribution, and evaluation of application applicability on specific DNA sequences.
Preparation of DNA with local DNA structures
Lofítková, Ellen ; Pernicová, Iva (referee) ; Brázda, Václav (advisor)
In this thesis I focused on quadruplexes and cruciforms formed by DNA. Plasmids pBluescript and others derived from it by inserting oligonucleotid sequences were studied. Sequences forming quadruplexes and cruciforms were found by in silico analysis by QGRS Mapper and Palindrome analyser. Plasmids were transformed into E. coli, isolated and then cleaved with enzymes S1 nuclease and restriction endonuclease ScaI. Cleaving with S1 nuclease predicated presence of local structure. Combined S1/ScaI cleavage did not bring satisfying results due to lost of DNA during purification.
Optimization of G-Quadruplex Identification Algorithm
Labudová, Dominika ; Martínek, Tomáš (referee) ; Hon, Jiří (advisor)
Identification of G-quadruplexes in DNA has been the interest of many studies  in recent years. As a result, many identification tools were created. This bachelor's thesis focuses on analysis and optimization of a tool called pqsfinder along with creating a web interface for this tool. The optimization provided significant increase in the algorithm's speed and ability to process long DNA sequences. The web interface was designed and implemented using modern and effective technologies with emphasis on the user friendliness of the web application.
Gout diet
KOZÁK, Martin
This Bachelor's thesis, that is concerned with the disease gout, is divided into 3 parts. Theoretical part of this thesis is dedicated to the description of this disease, including its treatment and related diet measures, which have to be followed. Part of this study is a research of respondents with gout disease. This research was made as an interview with the respondents and it discovers necessary information including their diet. Results of this research are described at the end of this thesis and it shows that gout disease cannot be treated only with pharmaceutical means, but it is important to follow appropriate diet including an overall change of a life style
The thermodynamics of DNA-hairpin formation
Sgallová, Ráchel ; Římal, Václav (advisor) ; Profant, Václav (referee)
Serum response factor (SRF) is a transcription factor which binds to a highly conserved DNA sequence called the CArG box. According to the nucleotide sequence of CArG box it could form a hairpin structure or a cruciform. In this master thesis, the structure of the CArG box in a human gene c-fos was studied by nuclear magnetic resonance. 1 H spectra at temperatures 274{356 K, two-dimensional 1 H{1 H NOESY spectra, and two-dimensional 1 H{13 C HMBC spectra for DNA sequences with lengths of 12, 14 and 16 nucleoti- des were acquired. The thermodynamic parameters of formation of the secondary structure in the samples were determined from the measured temperature depen- dencies. The hairpin formation in the samples was con rmed based on the NOESY spectra and the lack of dependency of the melting temperature on concentration. The observed difference of the secondary structure from B-DNA could serve as a possible explanation of the high a nity of SRF to CArG box. 1
A Preliminary Study of Modification of 7-Deazaadenine with a Complex of Osmium Tetroxide with 2,2 '-Bipyridine
Vítová, Lada ; Havran, Luděk ; Fojta, Miroslav ; Šedo, O. ; Zdráhal, Z. ; Vespalec, Radim
Reactivity of a purine nucleic base analogue 7-deazaadenine (A*) in short oligodeoxynucleotide (ODN) towards an osmium tetroxide complex with 2,2'-bipyridine (Os, bipy) was investigated by means of electrochemistry, capillary electrophoresis and MALDI-TOF mass spectrometry. Electrochemical measurement, electrophoretic analyses and mass spectrometric analyses of reaction mixture proved that ODN with an A* residue yields an osmium adduct with properties similar to those exhibited by the well-known adduct of thymine.
Petr, Marek ; Bažantová, Pavla ; Adámik, Matěj ; Kejnovská, Iva ; Dvořáková, Zuzana ; Vorlíčková, Michaela ; Pečinka, Petr ; Brázdová, Marie
In this work we performed DNA polymerase stop assays while using template DNA derived from promoter regions of VEGF and c-Myc proto-oncogenes under variety of experimental conditions. Partial stopping of DNA synthesis along the template strand was observed in the presence of K+ ions due to formation of stable G-quadruplex structures. In contrast, Na+ ions alone were unable to stabilize G-quadruplexes to stop the reaction at their site. These data suggest that K+ and Na+ ions, which are both known to stabilize G-quadruplexes, do this in different manner or extent.
Haroniková, Lucia ; Špaček, Jan ; Fojta, Miroslav
In this work, we present a new qualitative approach of detection of PCR products using electrochemistry on pencil electrodes. PCR products with an incorporated biotin-labeled dNTP (dCTP in this study) are detected via conjugated streptavidinealkaline phospatase. 1-Naphthyl phosphate (1-NP), which is dephosphorylated by alkaline phosphatase to release 1-naphthol, was used as a substrate in electrochemical detection of the PCR product. Voltammetric measurement on disposable pencil electrode is a very cheap and easy to use method. The system was optimized for plasmid DNA PCR product with potential to detect human genome DNA products and possible application in gene deletion monitoring.
Primer Extension Reaction at the Gold Electrode Surface
Vidláková, Pavlína ; Havran, Luděk ; Fojta, Miroslav
One option of covalent DNA labeling is incorporation of chemically modified nucleotides using corresponding deoxynucleotide triphosphates into DNA molecules using polymerase-catalyzed primer extension. Primer extension is usually performed in solution and then the product is analyzed, often after a suitable separation. In our study we tested the possibility to prepare oligonucleotides with enzymatically incorporated anthraquinone labeled nucleotides using primer extension on templates immobilize at a gold electrode surface.

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