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Methods for gene prediction in prokaryotic genomes
Nykrýnová, Markéta ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This bachelor thesis deals with methods of gene prediction in prokaryotic genomes. First part of the thesis introduces prokaryotic cell, its genome, expression of genetic information and methods for gene prediction. Following part describes three software products for gene prediction. Chosen software was tested against specific genome and next chapter presents obtained results. The last part describes program called Gene_finder and its results.
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Gene regulatory network inference based on mutual information in non-model organisms
Pirkl, Petr ; Sedlář, Karel (referee) ; Musilová, Jana (advisor)
The thesis is focused on summary of laboratory methods for determining gene expression, data preprocessing procedures and possible tools used to infere gene regulatory networks. Furthermore, the thesis handles with the pre-processing of data. It means create count table and normalize it. It was use data from the non-model organism Clostridium beijerinckii NRRL B-598. The main parts of the thesis are designed an algorithm for the creation of a gene regulatory network using mutual information and its implementation in the R language. This include testing the algorithm on data from the non-model organism and the gold standard.
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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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Molecular Characterisation of Parvalbumin Gene: Evolutionary Insights and Forensic Applications for Fish Species Identification and Authentication
Mukherjee, Subham ; Horká, Petra (advisor) ; Kalous, Lukáš (referee) ; Flajšhans, Martin (referee)
Abstract Parvalbumin (pvalb), a low molecular weight calcium-binding protein, plays a crucial role in regulating Ca2+ switching in fast-twitch muscle fibres and has been identified as a major cause of fish-induced food allergies. The molecular evolution of pvalb genes in teleost fish and its cause, duplication of the whole genome, was investigated, revealing high diversity and complex gene repertoires, making detection and identification challenging. This study provides robust genomic evidence of the complex evolution of parvalbumin genes in teleost fish. In addition to its role as a potent allergen, the pvalb gene, a nuclear gene, can serve as a valuable molecular marker. Keeping this in mind, a real-time PCR assay is developed to detect and quantify two European anglerfish species simultaneously, Lophius piscatorius and Lophius budegassa, which are susceptible to illegal species substitutions in the global seafood trade. The assay targets the intronic region of the pvalb gene, demonstrating high specificity, efficiency, and robustness, making it a potential forensic tool to prevent food fraud and ensure the accurate identification of fish species. Furthermore, a standardised quantitative PCR-based method is presented for the β-pvalb gene in Lophius piscatorius, utilising a plasmid DNA calibrator...
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Function of the Tetratrico-peptide Thioredoxin-Like (TTL) gene family in root system development
Xin, Pengfei ; Soukup, Aleš (advisor) ; Vaňková, Radomíra (referee) ; Ovečka, Miroslav (referee)
The root system performs fundamental plant functions such as uptake of nutrients and water, anchoring in the substrate, and interacting with the rhizosphere abiotic and biotic interactions, playing an important role in meeting the food security needs of today's world. Lateral roots (LR) are essential components of the plant root system. We have identified the TETRATRICOPEPTIDE-REPEAT THIOREDOXIN- LIKE 3 (TTL3) gene as being related to LR emergence and later development. Loss-of-function of TTL3 results in a reduced number of emerging LRs due to delayed development of lateral root primordia (LRP). In the Arabidopsis TTL gene family, except for TTL2 which was specifically involved in male gametophyte development, the expressions of the other three TTLs (TTL1, TTL3 and TTL4) were all related to root growth and development. The temporal and spatial distribution of TTL3 expression was consistent with its role in LR growth preceding and following LRP emergence. In the subcellular localization of TTL1, TTL2 and TTL3, all were shown to be associated with microtubules during the transient transformation of tobacco leaves, and TTL3 was confirmed to interact with microtubules. TTL3 was also associated with the endomembrane system and was known to be interacting with the brassinosteroid (BR) signaling pathway....
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Audio effect based on signal spectrum modification
Vejvoda, Zdeněk ; Sysel, Petr (referee) ; Schimmel, Jiří (advisor)
The thesis describes the design and the engineering solution of a hardware electronic sound effect that is a mixture of a frequency shifter and a delay effect. Electronic music intruments, sound effects and particularly modular synthesizer of the Eurorack standard are introduced. The firmware, developed utilizing the Max Gen environment and running on an ARM chip, prompted an examination of the Max platform. Finally, the thesis explores the calculations and processes required to construct a fully functional effect module. The device was assembled, tested and measured.
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Variabilita polymorfizmu v genu FABP3 a jeho asociace s ukazateli kvality masa u prasat
Boleslavová, Štěpánka
The aim of the study was to study the variability of the gene in the population FABP3 pig breed Czech large white. Analyze their association with indicators of pork production. Gene FABP3 belonging to multigene families FABP (fatty acid binding proteins affecting the transport of long chain fatty acids). Analyzed polymorphism was at position X98558:g.1321G>C in the 5'UTR region. The relative frequencies of genotypes were: HH = 0,87, Hh = 0,13. hh genotype was not detected in the monitored individuals. The values of the relative frequencies of alleles were as follows: H = 0,93 h = 0,07. Based on the association analysis showed a statistically significant difference between genotypes for stearic acid and linoleic acid. Highly statistically significant difference was observed with palmitic acid.
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Clinical significance of the rs4646994 polymorphism in the ACE gene
BÍCHOVÁ, Simona
The present bachelor thesis deals, as it is obvious from the title, with one particular polymorphism rs4646994 in the ACE gene and its clinical significance. The ACE gene, consisting of 26 exons, is localized on chromosome 17q23 and its name ACE stands for angiotensin converting enzyme. This enzyme is capable of breaking down proteins and is part of the renin-angiotensin system, which regulates blood pressure and fluid and salt balance in the body. The principle is to split a protein called angiotensin I into angiotensin II. This then causes the blood vessels to narrow (constrict), leading to an increase in blood pressure. This protein also stimulates the production of the hormone aldosterone, which triggers the absorption of salts and water by the kidneys. The increased amount of fluid in the body subsequently increases blood pressure. In addition, angiotensin II may also play a role in kidney development. The selected ACE rs4646994 polymorphism is of great interest in terms of various diseases (e.g. COVID-19, nephropathy in diabetes mellitus, polycystic ovary syndrome, etc.) It may also play an important role in Alzheimer's disease, which is the focus of the practical part of this bachelor thesis. The investigation of the rs4646994 polymorphism in the ACE gene was carried out in a selected group of 61 patients with a diagnosis of dementia by end-point PCR. The data obtained were then statistically processed and compared with a control group of patients without a diagnosis of dementia. The results were then compared with available scientific publications.
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Gene regulatory network inference based on mutual information in non-model organisms
Pirkl, Petr ; Sedlář, Karel (referee) ; Musilová, Jana (advisor)
The thesis is focused on summary of laboratory methods for determining gene expression, data preprocessing procedures and possible tools used to infere gene regulatory networks. Furthermore, the thesis handles with the pre-processing of data. It means create count table and normalize it. It was use data from the non-model organism Clostridium beijerinckii NRRL B-598. The main parts of the thesis are designed an algorithm for the creation of a gene regulatory network using mutual information and its implementation in the R language. This include testing the algorithm on data from the non-model organism and the gold standard.
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