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Dynamic metabolomic prediction from genetic variation
Nemčeková, Petra ; Weckwerth, Wolfram (referee) ; Schwarzerová, Jana (advisor)
Hordeum vulgare, tak ako mnoho ďalších plodín, trpí redukovaním genetickej rôznorodosti spôsobeným klimatickými zmenami. Preto je potrebné zlepšiť účinnosť jeho kríženia. Oblasť záujmu sa v poslednej dobe obracia na výskum nepriamych selekčných metód založených na výpočetných predikčných modeloch. Táto práca sa zaoberá dynamickou metabolomickou predikciou založenou na genomických dátach, ktoré pozostávajú z 33,005 jednonukleotidových polymorfizmov. Metabolomické dáta zahŕňajú 128 metabolitov 25 rodín Halle exotického jačmeňa. Hlavným cieľom tejto práce je vytvoriť metabolomické predikcie dynamických dát pomocou rôznych metód, ktoré boli vybrané na základe rôznych publikácií. Vytvorené modely napomôžu predikcii fenotypu alebo odhaleniu dôležitých vlastností rastliny Hordeum vulgare.
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Image segmentation of ultrasound images
Schwarzerová, Jana ; Odstrčilík, Jan (referee) ; Mézl, Martin (advisor)
This bachelor’s thesis deals with basic description of ultrasonography, principles of contrast-enhanced imaging and application of segmentation methods in ultrasound problematics. Some individual methods were implemented in Matlab, version R2015b. Algorithms were tested on synthetic images data, on ultrasound phantom images data and on real ultrasound images. Then the thesis was extended by ultrasound sequences segmentation.
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Concept drift in metabolomic analysis
Koštoval, Aleš ; Provazník, Ivo (referee) ; Schwarzerová, Jana (advisor)
This bachelor thesis deals with machine learning, specifically the analysis of the concept drift. This is an unwanted phenomenon that can be detected in predictive models. Through detection followed by correction of the concept drift, predictive models become more reliable and can respond adequately to input data representing dynamic information. Metabolomic data can be considered a suitable representative of such data. Metabolomic data and their analysis can help to detect diseases such as diabetes mellitus or cancer early. In the first part of this bachelor thesis, the theoretical background of concept drift analysis and metabolomics analysis are described. The second part discusses the process of modeling predictive classifiers and implementing algorithms for concept drift detection. The practical part of the work was implemented in the Python programming language. Finally, the second part describes the results obtained and their discussion.
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Gene regulation in Clostridium beijerinckii NRRL B-598
Schwarzerová, Jana ; Jurečková, Kateřina (referee) ; Sedlář, Karel (advisor)
Diplomová práce se zabývá studiem genové regulace v Clostridium beijerinckii NRRL B-598, pro následné odvození genové regulační sítě bakterie C. beijerinckii NRRL B-598. V teoretické části této práce je uvedena obecná nomenklatura problematiky genové regulace se zaměřením na nomenklaturu genových regulačních sítí. Následně jsou zde popsané laboratorní metody, sloužící pro získání vhodných dat popisující expresi genů. Tato data jsou základem pro studium genové regulace a návrhy genových regulačních sítí. Práce se zaměřuje především na technologii RNA-Seq a stručný popis laboratorních dat získaných ze zmíněné bakterie C. beijerinckii NRRL B-598. V praktické části se práce zabývá předzpracováním těchto surových laboratorních dat a následným studiem genové regulace se zaměřením na odvození operonů a vytvoření prvních genových regulačních sítí pomocí různých přístupů pro C. beijerinckii NRRL B-598.
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Operon structures inference in genome-wide analysis
Nejezchlebová, Julie ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor thesis is devoted to the problem of derivation of operon structures and creation of a software tool that allows prediction of operon structures. The tool both predicts operons based on gene expression information, but also refines already predicted operons with gene expression information. The tool is tested on the bacteria Escherichia coli BW25113 and Clostridium beijerinckii NRRL B-598. The theoretical part is devoted to description of operon structure and function, genome sequencing, transcriptome analysis, Clostridium beijerinckii NRRL B-598, Escherichia coli BW25113 and already available online tools for inferring operon structures. In the practical part of the thesis, the pre-processing of raw transcriptomic data to obtain a suitable format for the prediction of operon structures, testing of online tools and the actual implementation of the tool itself are discussed.
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Detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria
Vancová, Kateřina ; Schwarzerová, Jana (referee) ; Čejková, Darina (advisor)
This thesis deals with a detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria. Antimicrobial resistance (AMR) in bacteria is a growing threat to public health globally. In these bacteria, AMR genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. The work describes the horizontal gene transfer, the issue of antimicrobial resistance and the database for the detection of AMR genes and MGEs. After that, the detection and analysis of AMR genes and MGEs in anaerobic bacteria was done. Almost half of them contained at least 1 gene coding for antibiotic or heavy-metal resistance, 112 different genes overall. Then, 66 different MGEs were detected, 4 of which carried 6 different AMR detected genes.
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Detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria
Vancová, Kateřina ; Schwarzerová, Jana (referee) ; Čejková, Darina (advisor)
This thesis deals with a detail analysis on antibiotic and heavy-metal resistance genes and horizontal gene transfer traits in anaerobic bacteria. Antimicrobial resistance (AMR) in bacteria is a growing threat to public health globally. In these bacteria, AMR genes are often associated with mobile genetic elements (MGEs), which promote their mobility, enabling them to rapidly spread throughout a bacterial community. The work describes the horizontal gene transfer, the issue of antimicrobial resistance and the database for the detection of AMR genes and MGEs. After that, the detection and analysis of AMR genes and MGEs in anaerobic bacteria was done. Almost half of them contained at least 1 gene coding for antibiotic or heavy-metal resistance, 112 different genes overall. Then, 66 different MGEs were detected, 4 of which carried 6 different AMR detected genes.
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Comprehensive analysis of putrescine metabolism in A thaliana using GWAS, genetic risk score, metabolic modelling and data mining
Schwarzerová, Jana ; Bartoň, Vojtěch ; Walther, Dirk ; Weckwerth, Wolfram
Polyamines are known to be functionally involvedin plant responses to stress conditions. Despite a large amount ofphysiological and genetic data, the mode of action of polyamines,especially putrescine, at the molecular level still remains unclear.An increasing number of studies point to a role of putrescine instress defense of plants due to influencing the formation of reactiveoxygen species (ROS) in cellular stress conditions. Moreover,putrescine has been found to modulate abscisic acid (ABA)biosynthesis at the transcriptional level in response to lowtemperature, revealing a novel mode of action of polyamines asregulators of hormone biosynthesis. This study presents a newholistic approach towards the analysis of putrescine metabolismusing genome-wide association studies and the calculation ofgenetic risk scores extended by Boolean analysis in metabolitesnetwork as well as data mining from available databases andliterature. It can lead to a better understanding of biologicalprocesses involved in adaptation of plants to environmentalchanges.
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Correction of the concept of drift in prediction models
Michálková, Eva ; Provazník, Valentine (referee) ; Schwarzerová, Jana (advisor)
The main goal of this bachelor thesis is the analysis of concept drift in metabolomics. Concept drift is an undesirable phenomenon and can be caused by nonstationary data. It can have a negative impact on the performance and reliability of predictive modelling. This challenge can be solved by concept drift detection and subsequent correction. One of the fields where this issue has recently emerged is metabolomic diagnostics. Metabolomic data analysis can lead to early detection of several serious diseases, which can help with the recovery process. When diagnosing an illnes predictive models present a way to make the process more efficient, faster and give the option of personalization. The first part of this thesis specifies concept drift, it’s detection and correction methods and the importance of metabolomics and prediction models. The second part deals with the implementation of some available algorithms for concept drift detection and correction and the implementation of automatic concept drift correction. Finally, in the second part results and their discussion are described.
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Analysis of horizontal transfer of genetic components using static network analysis
Labanava, Anastasiya ; Jurečková, Kateřina (referee) ; Schwarzerová, Jana (advisor)
The bachelor's thesis focuses on the issue of horizontal genetic elements transfer between bacteria of different strains and the software analysis implementation that enables horizontally transferred genes identification. The packages and tools used were tested on a dataset of bacterial genomes from several strains. The thesis’ theoretical part provides a detailed description of the genetic components transfer between bacteria and describes modern laboratory techniques that enable genome sequencing in various ways. In the practical part, the thesis deals with the preprocessing of genomic files to obtain suitable data for annotation. To detect the horizontal transfer of genetic elements between bacteria, a script is introduced, which organizes annotated bacteria to tables and searches for the same genes in their genomes that, under theoretical assumptions, were horizontally transferred. Furthermore, the gene transfer is visualized using tools that graphically represent phylogenetic relations between bacteria. In the final step, bacterial genomes are connected into networks, and based on their static analysis, a discussion is conducted on the results accuracy and the success of the proposed analysis.
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