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CNV detection in bacterial genomes
Lacinová, Michaela ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
This master thesis deals with analysis of structural variation of genome and with methods of its sequencing across all generations. Subsequently it contains a description of copy number variation and methods of its detection. The experimental part focuses on algorithm proposal for CNV detection according analysis and testing of uneven coverage in genome, variable representation of GC content and distance of sequence reads. Finally, the algorithm for detecting copy number variation is tested on genomic data of bacteria Klebsiella pneumoniae.
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Signal processing based methods for genome assembly refinement
Jugas, Robin ; Provazník, Ivo (referee) ; Sedlář, Karel (advisor)
The diploma thesis deals with sequencing methods and genome assembly methods including usage of numerical representations. The theoretical part of thesis describes the history of DNA research, generations of sequencing methods, the assembly methods themselves and definiton of numerical representations. Numerical represenatations serve to convert character form of DNA to numerical form and so allow to use digital signal processing methods. There is an algorithm for genome assembly using numerical represenatation proposed in thesis, which is later tested at sequence data.
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Detekce patogenů lilku bramboru přežívajících v půdě
Valkovičová, Nikola
The bachelor's thesis dealt with the detection and sequencing of soil-borne pathogens of pota-to eggplant. The focus is mainly on pathogens of the genus Fusarium. These pathogens cause such potato rot, which forms white mycelium coatings and subsequently mummifies, that it is not suitable for consumption and the yield is reduced. One of the most accurate methods was chosen for the detection of pathogens – PCR. For the detection of Fusarium pathogens from other potato tubers, conventional PCR was used with non-specific primers ITS4 and ITS5 annealing to the region between the genes that code for ITS4 and ITS5 RNA. For the detection of pathogens from the soil, real–time PCR was chosen with primers ITS1F and AFP346 sitting in the region that encode nRNA and space bars ITS1 and ITS2. The tested soil was artificially inoculated with an unknown isolate of the genus Fusarium obtained from a potato tuber and a collection isolate of Fusarium solani var. coeruleum. Se-quencing confirmed infection of the potato tuber with Fusarium culmorum, clarifying the dif-ficulty of quantification.
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Effect of TNF-α inhibitors on microbiota composition and immune response in patients with inflammatory bowel disease
Mihula, Martin ; Jirásková Zákostelská, Zuzana (advisor) ; Grobárová, Valéria (referee)
One of the most common used therapies in inflammatory bowel diseases (IBD) treatment are inhibitors of a cytokine TNF-α. Nevertheless, up to one third of IBD patients stop respond to this therapy for unknown reason. In these days, there are not any ideal biomarkers which could predict patient's long- term response to anti-TNF-α therapy. Because the gut microbiota composition changes are tightly related to the pathogenesis of IBD, my aim in this thesis was to find out if these changes in composition are happening also due the therapy by inhibitors of TNF-α as well. Moreover, I tried to find out if there are changes in production of serum biomarkers related to the gut barrier damage and to the immune response associated with microbial translocation. Also, I focused on the immune response of IBD patients against common gut commensal bacterial antigens during the anti-TNF-α therapy. In our study, we collected for these purposes stool or blood samples from 46 IBD patients before the therapy and at 38th week from the start of the therapy and 39 healthy controls. I found that IBD patients had higher bacterial diversity (α-diversity) as well as different bacterial composition across observed groups (β-diversity) at 38th week of the anti-TNF-α therapy than before the therapy. When I divided IBD patients...
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Gene expression analysis on a subgene level
Kloda, František ; Fišer, Karel (advisor) ; Novotný, Marian (referee)
RNA sequencing allows investigation of expression of singular genes in cells. It is possible to interpret the arisen data on multiple levels, each level providing a different type of information. Apart from measuring expression of whole genes, it is possible to quantify expression of singular exons, or transcripts (gene isoforms), which allows more detailed study of regulatory mechanisms. The main difference between approaches is in determining the origin of short reads. This step is significantly more complex in analysis of expression of transcripts, as transcripts derived from the same gene have typically larger rate of sequential similarity. In this thesis, we describe eleven tools for subgene level expression analysis a as comparison we have tested three of these tools on real patient data. The results provided by all three tools proved to be very similar with the greatest difference being the time needed for the analysis.
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Typing of bacterial populations based on methylation site detection
Hlavatá, Kristína ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Táto bakalárska práca sa zameriava na detekciu metylácií DNA a vývoj metodiky typizácie bakteriálnych kmeňov. DNA metylácie hrajú kľúčovú úlohu ako regulačný mechanizmus v genóme, ktorý ovplyvňuje konečné vlastnosti organizmov. Použili sme DeepSignal2 na detekciu metylačných vzorov v 10 kmeňoch Klebsielly pneumoniae. Okrem toho sme navrhli metódu typizácie na základe identifikovaných metylácií pre kategorizáciu bakteriálnych kmeňov. Táto práca prispieva k zlepšeniu našeho chápania regulačných mechanizmov v bakteriálnych genómoch a predstavuje nový prístup k typizácii kmeňov pomocou vzorov metylácie DNA. Poskytuje cenné poznatky o charakterizácii a klasifikácii bakteriálnych kmeňov na základe ich metylómov.
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Antibiotic resistance profile determination in hybrid assembled bacterial genomes
Dzurčaninová, Natália ; Škutková, Helena (referee) ; Nykrýnová, Markéta (advisor)
Antibiotická rezistencia je vážny problém vo väčšine spôsobený zmenami v bakteriálnom genóme. Získavanie a uchovávanie spoľahlivých bakteriálnych genomických dát je preto nevyhnutné pre štúdium mechanizmov a prenosu antibiotickej rezistencie. Táto práca popisuje bakteriálny genóm, antibiotickú rezistenciu a nástroje pre jej identifikáciu spolu s procesmi nevyhnutnými pre zisk genómov, sekvenáciu a skladanie. Sústreďuje sa na hybridné skladanie genómov spravidla vysoko rezistentných baktérií Klebsiella pneumoniae a ich nasledujúcich analýz. Cieľom týchto analýz je skonštruovať profily antibiotických rezistencií a určiť fylogenetickú príbuznosť genómov.
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Typing of bacterial populations based on methylation site detection
Hlavatá, Kristína ; Sedlář, Karel (referee) ; Škutková, Helena (advisor)
Táto bakalárska práca sa zameriava na detekciu metylácií DNA a vývoj metodiky typizácie bakteriálnych kmeňov. DNA metylácie hrajú kľúčovú úlohu ako regulačný mechanizmus v genóme, ktorý ovplyvňuje konečné vlastnosti organizmov. Použili sme DeepSignal2 na detekciu metylačných vzorov v 10 kmeňoch Klebsielly pneumoniae. Okrem toho sme navrhli metódu typizácie na základe identifikovaných metylácií pre kategorizáciu bakteriálnych kmeňov. Táto práca prispieva k zlepšeniu našeho chápania regulačných mechanizmov v bakteriálnych genómoch a predstavuje nový prístup k typizácii kmeňov pomocou vzorov metylácie DNA. Poskytuje cenné poznatky o charakterizácii a klasifikácii bakteriálnych kmeňov na základe ich metylómov.
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Antibiotic resistance profile determination in hybrid assembled bacterial genomes
Dzurčaninová, Natália ; Škutková, Helena (referee) ; Nykrýnová, Markéta (advisor)
Antibiotická rezistencia je vážny problém vo väčšine spôsobený zmenami v bakteriálnom genóme. Získavanie a uchovávanie spoľahlivých bakteriálnych genomických dát je preto nevyhnutné pre štúdium mechanizmov a prenosu antibiotickej rezistencie. Táto práca popisuje bakteriálny genóm, antibiotickú rezistenciu a nástroje pre jej identifikáciu spolu s procesmi nevyhnutnými pre zisk genómov, sekvenáciu a skladanie. Sústreďuje sa na hybridné skladanie genómov spravidla vysoko rezistentných baktérií Klebsiella pneumoniae a ich nasledujúcich analýz. Cieľom týchto analýz je skonštruovať profily antibiotických rezistencií a určiť fylogenetickú príbuznosť genómov.
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Metagenomic analysis of animal gut microbioma based on diet
Spanakis, Martin ; Čejková, Darina (referee) ; Bartoň, Vojtěch (advisor)
This bachelor’s thesis deals with the sequencing of the microbiome and its composi- tion. It focuses on the gut microbiome of animals, which differs among animals with different diets. The work describes theoretical knowledge about metagenomic analysis of the microbiome, such as sampling procedures, various sequencing methods and data processing. The practical part of the work includes the preparation of the dataset, which includes the collection of data and their preparation for the following metagenomic anal- ysis. The result of the work is the taxonomic classification of bacterial species in the samples and the analysis of their diversity according to the type of diet of individual animals.
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