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Microarray Data Interpretation
Ludwig, Petr ; Šilhavá, Jana (referee) ; Smrž, Pavel (advisor)
This Bachelor thesis explains the basics of biochip or microarray data interpretation, starting with short introduction to genetics, especially genetic information significance evaluating. The focus was set mainly on the set of scripts transforming and analyzing the sample data. The data used in this thesis are a result of biochip analysis of the Colon Tumor tissues. The secondary result represents disclosing the main marker for this particular type of cancer, the primary result is evaluation of marker significance in the context of signaling pathways. The resulting pathways are sorted by relevance.
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Diagnostics of genom conditioned diseases with the use of micro- and nanoparticles
Mondeková, Věra ; Prášek, Jan (referee) ; Provazník, Ivo (advisor)
The bachelor´s thesis discusses possibilities of viral genome´s detection through use of biosensors, more specifically through use of magnetic particles. The introductory part consists of brief characteristic of viruses, mentioned as originator of genom conditioned diseases, followed by chapters related to selected methods of nucleic acid´s extraction and analysis. The main part is dedicated to magnetic particles. The practical part of thesis deals with possibility of use of biosensors in specific viral pathogen´s detection, selection of biocompatible molecules suitable for magnetic particle modification and description of specific DNA sequence isolation procedure through use of magnetic particles.
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Analysis of intron sequence variability
Kukačková, Hana ; Provazník, Ivo (referee) ; Kubicová, Vladimíra (advisor)
This bachelor thesis reviews genetic expression, the main characteristics of introns, their importance, and the methodology of their recognition. Practical part focuses on intron variability analysis and conservative sequences searching. In the beginning, there is a structure of nucleic acids with their chemical and physical characteristics reviewed, follow by gene expression description with all steps – transcription, posttranscriptional splicing and translation. Afterwards, there is an analysis of introns importance, introns evolution theories and similarities among different organisms mentioned, follow by some introns recognition methods. Practical part is focused on the initial and terminal regions of introns and conservative dinucleotide sequences verifying. The thesis studies intron – exon and exon – intron boundaries. The last part tries to suggest new potentially conservative sequences – patterns, search for them and check their conservativeness.
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Molecular Signature as Optima of Multi-Objective Function with Applications to Prediction in Oncogenomics
Aligerová, Zuzana ; Maděránková, Denisa (referee) ; Provazník, Ivo (advisor)
Náplní této práce je teoretický úvod a následné praktické zpracování tématu Molekulární signatura jako optimální multi-objektivní funkce s aplikací v predikci v onkogenomice. Úvodní kapitoly jsou zaměřeny na téma rakovina, zejména pak rakovina prsu a její podtyp triple negativní rakovinu prsu. Následuje literární přehled z oblasti optimalizačních metod, zejména se zaměřením na metaheuristické metody a problematiku strojového učení. Část se odkazuje na onkogenomiku a principy microarray a také na statistiku a s důrazem na výpočet p-hodnoty a bimodálního indexu. Praktická část je pak zaměřena na konkrétní průběh výzkumu a nalezené závěry, vedoucí k dalším krokům výzkumu. Implementace vybraných metod byla provedena v programech Matlab a R, s využitím dalších programovacích jazyků a to konkrétně programů Java a Python.
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Hardware Acceleration of Algorithms for Approximate String Matching
Nosek, Ondřej ; Kořenek, Jan (referee) ; Martínek, Tomáš (advisor)
Methods for aproximate string matching of various sequences used in bioinformatics are crucial part of development in this branch. Tasks are of very large time complexity and therefore we want create a hardware platform for acceleration of these computations. Goal of this work is to design a generalized architecture based on FPGA technology, which can work with various types of sequences. Designed acceleration card will use especially dynamic algorithms like Needleman-Wunsch and Smith-Waterman.
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Reactive modifications of RNA for bioconjugations with proteins and new enzymatic methods for the synthesis of base-modified RNA
Brunderová, Mária ; Hocek, Michal (advisor) ; Míšek, Jiří (referee) ; Vaňáčová, Štěpánka (referee)
This doctoral thesis focuses on the enzymatic synthesis of base-modified RNA probes with diverse functional groups, including reactive cross-linking, hydrophobic and fluorescent moieties, or affinity tags. The construction of nucleobase-modified oligonucleotides is accomplished either through conventional in vitro transcription with T7 RNA polymerase or by an innovative approach leveraging engineered mutant DNA polymerases and primer extension reaction (PEX). In the first section of the thesis, a novel ribonucleoside triphosphate building block with reactive chloroacetamide functionality was synthesised using an aqueous Pd-catalysed Sonogashira cross- coupling reaction, directly applied on iodinated nucleotide. The chloroacetamide modified triphosphate was then tested as a putative substrate for T7 RNA polymerase in in vitro transcription reaction, aiming to construct RNA probes with one or multiple reactive groups. The selectivity of chloroacetamide- modified RNA for thiol-, or cysteine-, and histidine-containing (bio)molecules was demonstrated by model bioconjugation reactions and cross-linking experiments with three RNA-binding proteins of diverse structures and functions. The efficient formation of RNA-protein covalent adducts was confirmed by western blot or gel, and mass spectrometry analyses...
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Biophysical Characterization of Coronaviral nsp14 Inhibition
Trembulaková, Pavla ; Bouřa, Evžen (advisor) ; Dejmek, Milan (referee)
RNA virus SARS-CoV-2 caused worldwide pandemic of severe disease COVID-19 which lasted more than a year. Repair mechanisms of this virus during replication process significantly reduce efficiency of nucleotide analog drugs, eg. remdesivir. Nonstructural protein (nsp) 14 and nsp10 form a complex which acts as an exonuclease enzyme and will be furthrer referred to as an ExoN complex. This complex can probably cause lower efficiency of incorporation of nucleotide analogs compared to viruses without exonuclease enzymes. The two-protein complex with active site on nsp14 containing two magensium ions seems like a good target for testing potent inhobitors. Among possible inhibitors of SARS-CoV-2 exonuclease complex are isobavachalcone and sofalcone. According to published studies, those small organic molecules chelate magensium ions in active site of exonulease part in nsp14. This results in inactivation of ExoN complex active site in nsp14 structure and disables the catalytic function which acts as repairing element in RNA synthesis process. This tesis focuses on characterization of inhibition of protein complex nsp14 and nsp10 in presence of small selected molecules, isobavachalcone and sofalcone. Exonuclease activity assays in presence of various RNA substrates were performed. Furthermore, there have been...
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Detekce a identifikace patogenu konopí setého (Cannabis sativa)
Jarošová, Natálie
The aim of this work was the detection and identification of Hop Latent Viroid in plants of Cannabis sativa. This Viroid, which may not have any symptoms on plants, as the name suggests. One of the few detection options is based on the principle of the polymerase chain reaction - PCR. Using the chloroform-phenol reaction, it was possible to isolate RNA of the Viroid, which was used as a template for cDNA and subsequently multiplied by the PCR method. After successful PCR, the samples were applied to an agarose gel and evaluated by comparison with a size marker. For subsequent testing of the pathogen detection and identification protocol, positive samples from Genetia BioSciences were added, and for testing real samples from the genotype collection from the Department of Plant Biology, plants with the presence and absence of Hop Latent Viroid were identified.
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