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Mutual similarity of aminoacid sequences in different organisms
Vysoudil, Ladislav ; Provazník, Ivo (referee) ; Škutková, Helena (advisor)
The aim of this semestral project is to try to study and describe work with sequences of proteins of different organisms, namely above all alligment sequences and evaluation of similarities of sequences. At the beginning of this work we deal with biochemistry of proteins, their constitution and structure. Further text go on with theory for work with sequential data, global, local and multiple assignment. At the last part we investigate possibilities of programme Matlab for aforesaid assignment.
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Identifying CpG islands in genomes of eukaryotes
Urbánková, Kateřina ; Provazník, Ivo (referee) ; Maděránková, Denisa (advisor)
Bachelor thesis deals with searching CpG islands in DNA. The theoretical part describes the structure and composition of deoxyribonucleic acid, chromosomes and genes. There is basic information about human and chimpanzees genome and specification of CpG islands. Practical part consists of a program that searches for CpG islands in sequences, it displayes and saves it. This work includes analysis of genes which are common for Homo sapiens, Pan troglodytes, Mus musculus and Bos taurus.
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Compression and analysis of digital video signals
Grúbel, Michal ; Slanina, Martin (referee) ; Kratochvíl, Tomáš (advisor)
This bachelor's thesis deals with technical parameters of chosen algorithms for video compression, especially MPEG-1, MPEG-2, MPEG-4 Part 14 and DivX. Whitin it there was created a special software in Matlab that compares frames differences between reference and evaluated sequence. For this purpose there were recorded short test sequences with different properties in time and frequency domain, which recording, compressing, decompressing and decompiling to single frames are described and shown in detail. The results of evaluation are processed in graphs and then described in writing. In final overall evaluation is stated which algorithm for video compression is optimal for which type of sequences that differ in properties in time and frequency domain.
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Image Motion Detection
Zítka, Michal ; Richter, Miloslav (referee) ; Horák, Karel (advisor)
This bachelor project dissert on detection of motion in image. Also sumary basic methods for detection of motion in image and method of segmentation using active contour. In practical section is attention paid to detection of motion in video camera screenshots.
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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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Compatibility of selected dental alloys with magnetic resonance imaging
Linetskiy, Igor ; Hubálková, Hana (advisor) ; Suchánek, Jakub (referee) ; Dostálová, Taťjana (referee)
Magnetic resonance imaging (MRI) is one of the up-to-date and perspective methods of diagnostic medical imaging. It is highly valued for absence of ionizing radiation, non-invasiveness, acquiring of highly accurate images of hard and especially soft tissues in any plane. It is a method of choice in central nervous system imaging. Nowadays it is used in diagnostics of other diseases in the maxillofacial area. The major shortcoming of MRI is interaction of magnetic fields of MRI system with metallic objects present in human body. As a result, this may lead to their heating, movement, and also to imaging artifacts. Since different metallic constructions (fixed bridges, dental implants, splints, plates, orthodontic appliances, etc.) are often used in the contemporary dentistry, the problem of their compatibility with MRI is relevant. The aim of this study was to validate the compatibility of dental alloys with MRI, classify the materials according to the degree of compatibility and to establish the range of their possible negative impact on quality of MRI in head and neck area. In order to find dental metals and alloys, General Health Insurance Company code- list, catalogues of manufacturers' and Prague dental labs were used. Measurement methods of magnetic susceptibility (MS), electric conductivity...
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Bioinformatics analysis of sequences required for localization of RNA during development
Naraine, Ravindra ; Šindelka, Radek (advisor) ; Fulková, Helena (referee) ; Tichý, Boris (referee)
The development of a complex organism from the fusion of two cells (oocyte and sperm) has been a fascinating aspect of developmental biology. It is now known that certain spatially and temporally regulated molecules tightly regulate embryogenesis. The asymmetrical gradient of these molecules within a given cell or within groups of cells helps to guide the differentiation of certain parts of the developing embryo. In fishes and frogs, the establishment of the maternal animal-vegetal transcript gradient within the egg produces the first developmental axis and subsequent formation of the ectoderm, mesoderm, and endoderm regions. Despite this important process, most of our knowledge on this initial animal-vegetal distribution in vertebrates has been limited primarily to the Xenopus laevis model, involved the analysis of only few transcripts and also analyzed only polar regions of the oocyte. This thesis aims to address this deficit in knowledge by leveraging high throughput analysis (RNA sequencing) to characterize and compare the maternal transcriptome and its sub-compartmentalization within the egg of four distantly related models. Additionally, we analyzed different stages of oocyte maturation to determine where the observed localization occurs. The models used were the African clawed frog (Xenopus...
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Barcoding of Czech butterflies
ŠKOPEK, Patrik
The aim of this thesis was to extract DNA of Czech butterflies and sequence their mitochondrial gene cytochrome c oxidase subunit I (i.e., the barcode), in order to uncover their genetic and intraspecific relationships and geographical differences. Moreover, I compared the sequences with data from other European countries. I extracted DNA from butterfly legs, amplified the target DNA fragment with PCR (polymerase chain reaction), and check the PCR product quality on an agarose gel. PCR products were sequenced. In total, I collated 500 sequences from 87 species (61.7% of the Czech fauna). Phylogenetic trees were built by maximum likelihood and Bayesian inference methods. To reveal the potential cryptic diversity and lineages, I used GMYC analysis. The results of GMYC were distributed into four groups: 71 species (81.6%) contained a single entity, two species pairs (4.6%) were merged into two entities, 10 species (11.5%) were split into more entities (potential cryptic diversity) and two species (2.3%) were both split and merged with a different species. To Czech samples of 33 Lycaenid species, I added database samples from Romania and Germany. Their relationships were compared based on a phylogenetic tree. In the case of 10 species (30.3%), data from one country was missing. In 19 species (57.7%), the Czech samples were related to both Romanian and German samples. One species (3%) was related to Romanian samples and one species to German samples. Two Czech species (6%) formed a separate branch in the tree. This work served as a preliminary study into the Czech butterfly mitochondrial diversity and barcoding efficacy, but more data is needed to complete the study.
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The mathematical theory of juggling
Búzik, Michal ; Slavík, Antonín (advisor) ; Karger, Adolf (referee)
Title: The mathematical theory of juggling Author: Michal Búzik Department: Department of Mathematics Education Supervisor: RNDr. Antonín Slavík, Ph.D. Abstract: This bachelor thesis is concerned with methods of mathematical descrip- tion of juggling. The main part deals with notation of simulation of throwing balls using integer sequences, so-called siteswaps. It indicates generating, mutual relations and ways of graphic interpretation of these sequences in diagrams. Summarized re- sults with generalization of all possible calculations of juggling sequences according to restrictive aspects are provided in this thesis. Beside usage of combinatorics and graph theory, there are also relations between juggling and braid theory, and change ringing interpreted. Keywords: juggling, sequence, siteswap
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The mathematical theory of juggling
Zamboj, Michal ; Slavík, Antonín (advisor) ; Halas, Zdeněk (referee)
Title: The mathematical theory of juggling Author: Bc. Michal Zamboj Department: Department of Mathematics Education Supervisor: RNDr. Antonín Slavík, Ph.D. Abstract: This diploma thesis extends the bachelor thesis of the same name. It deals with the graphic representation of juggling sequences by the cyclic diagram. Using the Burnside theorem and cyclic diagrams, we calculate the number of all genera- tors of juggling sequences. The relation between juggling and the theory of braids is described as well. The mathematical model of inside and outside throws is made from an empirical observation of trajectories of balls. Braids of juggling sequences and their attributes are provided using a real model of ladder. A sketch of the proof of the theorem that any braid is juggleable is given as well.
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