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Study of DNA-doxorubicine interaction by electrochemical methods on nanostructured electrodes
Přibyl, Jakub ; Fohlerová, Zdenka (referee) ; Kynclová, Hana (advisor)
Cancer diseases are one of the leading causes of mortality worldwide, for this reason, great attention anticancer drugs. Doxorubicin falls into the category of the most widely used cancer drugs. The method of electrochemical impedance spectroscopy were investigated properties of golds electrodes without deposit nanoparticles and electrodes with deposit gold nanoparticles. Using voltammetric measurements we detected doxorubicin and investigated the interaction of doxorubicin with oligonucleotides on gold electrodes without nanoparticles and electrodes modified with gold nanoparticles.
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Prediction of the Effect of Nucleotide Substitution Using Machine Learning
Šalanda, Ondřej ; Martínek, Tomáš (referee) ; Bendl, Jaroslav (advisor)
This thesis brings a new approach to the prediction of the effect of nucleotide polymorphism on human genome. The main goal is to create a new meta-classifier, which combines predictions of several already implemented software classifiers. The novelty of developed tool lies in using machine learning methods to find consensus over those tools, that would enhance accuracy and versatility of prediction. Final experiments show, that compared to the best integrated tool, the meta-classifier increases the area under ROC curve by 3,4 in average and normalized accuracy is improved by up to 7\,\%. The new classifying service is available at http://ll06.sci.muni.cz:6232/snpeffect/.
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Comparison of DNA isolation methods
ŠESTÁKOVÁ, Kristýna
Isolating DNA is crucial in genetic laboratories. I tis the first method of further steps to obtain DNA information. The isolation method requirements are high, Due to the similarity of DNA to other biopolymers, the method must exhibit high selectivity and also sensitivity due to the low DNA content of the biological material. The input sample from clinical practice is usually human blood and nuclear cells contained in it. This thesis describes why blood is most commonly used. From the volunteer blood obtained, DNA was isolated by four methods: salting out, based on a change in DNA solubility depending on the change in ion concentration in the solution; phenol-chloroform extraction, which is one of the cheapest and oldest methods; in addition, using a commercially available kit, a fast and simple method using DNA binding to a silicate surface; and isolating with an automated magnetic particle separator (Anzenbacher and Kovář, 1986). Each method has its advantages and disadvantages and its choice depends on the further handling of DNA. The most common criteria for choosing an isolation method is its time-consuming , the cost of the method, the yield and the purity of the DNA. In this thesis these requirements are compared amongst methods.
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Voltammetric Study of the Interaction of Genotoxic 2-Nitrofluorene with DNA at a Hanging Mercury Drop Electrode
Krejčová, Zuzana ; Vyskočil, Vlastimil (advisor) ; Nesměrák, Karel (referee)
In this Diploma Thesis, an interaction of genotoxic environmental pollutant 2-nitrofluorene with a double-stranded calf thymus DNA has been studied using a hanging mercury drop electrode (HMDE) as an electrochemical sensor. Two types of DNA damage were investigated and electrochemically detected (using cyclic voltammetry and differential pulse voltammetry): (i) The DNA damage caused by the direct interaction with 2-nitrofluorene and (ii) the DNA damage caused by short-lived radicals generated by the electrochemical reduction of the nitro group in 2-nitrofluorene. For the study of direct interaction, HMDE was modified by DNA and the interaction of DNA with 2-nitrofluorene was studied, after their incubation, right at the HMDE surface (adsorptive transfer stripping technique) or the DNA was preincubated with 2-nitrofluorene and, subsequently, the interaction was studied voltammetrically (DNA titration technique). Using both detection techniques, the formation of DNA - 2-nitrofluorene complex was observed and the mutual interaction was interpreted as an intercalation between the DNA base pairs, although such interaction was not clearly confirmed by UV-visible absorption spectroscopy. An electrostatic binding of 2-nitrofluorene on DNA sugar-phosphate backbone was partially formed at low concentrations of...
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Study of DNA-doxorubicine interaction by electrochemical methods on nanostructured electrodes
Přibyl, Jakub ; Fohlerová, Zdenka (referee) ; Kynclová, Hana (advisor)
Cancer diseases are one of the leading causes of mortality worldwide, for this reason, great attention anticancer drugs. Doxorubicin falls into the category of the most widely used cancer drugs. The method of electrochemical impedance spectroscopy were investigated properties of golds electrodes without deposit nanoparticles and electrodes with deposit gold nanoparticles. Using voltammetric measurements we detected doxorubicin and investigated the interaction of doxorubicin with oligonucleotides on gold electrodes without nanoparticles and electrodes modified with gold nanoparticles.
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Prediction of the Effect of Nucleotide Substitution Using Machine Learning
Šalanda, Ondřej ; Martínek, Tomáš (referee) ; Bendl, Jaroslav (advisor)
This thesis brings a new approach to the prediction of the effect of nucleotide polymorphism on human genome. The main goal is to create a new meta-classifier, which combines predictions of several already implemented software classifiers. The novelty of developed tool lies in using machine learning methods to find consensus over those tools, that would enhance accuracy and versatility of prediction. Final experiments show, that compared to the best integrated tool, the meta-classifier increases the area under ROC curve by 3,4 in average and normalized accuracy is improved by up to 7\,\%. The new classifying service is available at http://ll06.sci.muni.cz:6232/snpeffect/.
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