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MHC and KIR genotyping of macaques in HIV infection research
Matula, Jan ; Maděránková, Denisa (referee) ; Sedlář, Karel (advisor)
Modern research of viral diseases relies on genomic data processing. Not only is the sequence of a virus important, genomic sequence of specific receptors in affected organisms also plays an important role. In this paper, a novel package for processing of next generation sequencing data in infectious disease written using R/Bioconductor language is proposed. Functionality of the package, including implementation of advanced SSAHA algorithm for fast database searches, is demonstrated using genotyping of genes for MHC and KIR receptors of HIV positive macaques.
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Bioinformatic analysis of single nucleotide polymorphisms in the 1000 Genomes Project database
Parobková, Viktória ; Roy, Sudeep (referee) ; Provazník, Ivo (advisor)
Sekvenovanie celého ľudského genómu a nájdenie jeho variácii bolo výzvou počas mnohých rokov. Znalosť všetkých genetických variácií je pozoruhodne prospešná pri výskume chorôb. Táto práca je zameraná na genetické variácie človeka a ich dva hlavné výskumné projekty, The HapMap Project a The 1000 Genomes Project, ktoré pomohli v analýze chorôb. Prvá časť práce je venovaná teoretickému popisu projektov. V nasledujúcej časti práce sú popísané štruktúry databáz u oboch projektov a taktiež je predstavený online nástroj umožňujúci prehľadávanie a sťahovanie ich dát. Následne je prevedená štatistická, populačná a bioinformatická analýza štrukturálnych variácií produkovaných 3 fázou 1000 Genomes projektu.
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Bacterial genotyping based on the oligonucleotide melting temperature
Šandová, Hana ; Škutková, Helena (referee) ; Nykrýnová, Markéta (advisor)
This bachelor’s thesis deals with genotyping based on the oligonucleotide melting temperatures. In the theoretical part, DNA, typing, experimental and theoretical genotyping methods are described. The practical part of the thesis deals with a program that is designed to calculate the melting temperatures of sequences based on different methods, and the graphical user interface was created. In the following part, the measured melting temperatures of bacterial isolates of Klebsiella pneumoniae are compared to the theoretically calculated melting temperatures. In the last part of the thesis, the possibility of genotyping using cluster analysis based on the theoretical melting temperatures is explored.
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Automatic genotyping of bacteria by rep-PCR
Pelikánová, Veronika ; Maděránková, Denisa (referee) ; Škutková, Helena (advisor)
This thesis deals with automatic bacteria genotyping by rep-PCR method. Its theoretical part presents various methods of DNA typing, basic information on electrophoresis and modern electrophoretic approaches, including their problems, misleading data distortion. In order to automate typing, there has been introduced a program for phylogenetic sample classification from rep-PCR, also applicable for data from chip capillary electrophoresis. The program consists of three main parts: digitization, bandmatching and clustering apparatus to bacterial type classification. The result of the algorithm is a phylogenetic tree, which indicates the cluster of sapmles according to bacterial type. The program has a graphical user interface for possible use in the Children's Hospital. Finally, the program is tested with data from the Children´s Hospital.
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Genotyping of Klebsiella pneumoniae isolates
Nykrýnová, Markéta ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
This master thesis deals with typing of Klebsiella pneumoniae isolates. The first part of the thesis introduces molecular typing methods. Then bacterial genomes and Klebsiella pneumoniae are characterized. Following part describes data validation, assembly of genomes and proposed algorithm for finding genes with high variability. In last part obtained results are presented and validated on other genomes of Klebsiella pneumoniae.
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Metronidazole resistence in clinical cases of giardiasis.
Perglerová, Aneta ; Tůmová, Pavla (advisor) ; Uzlíková, Magdalena (referee)
Metronidazole (MTZ) targets a spectrum of anaerobic pathogens ranging from bacteria to eukaryotic parasites, including the protist Giardia intestinalis (Metamonada). Despite the long time and widespread use of MTZ, understanding giardiasis treatment failure (G-TF) is incomplete. Most of the knowledge was gained on laboratory-generated resistant lines or on clinical lines without data on the treatment outcome. In cooperation with Bulovka University Hospital in Prague, 70 giardiasis cases were followed between 2020-2023, of which 25.7% exhibited the G-TF. Giardia genotyping revealed that G-TF cases belonged to the same genetic group (assemblage B, mainly BIII); and G-TF cases were all imported, out of which 60% were from returning travellers from India. To test the hypothesis that resistance is genetically determined/associated with a transmissible genotype, genetic polymorphisms shared in Giardia G-TF samples in a set of genes involved in MTZ metabolism and detoxifications (NR1, NR2, prx1, hmp) were examined. The analysis revealed amino acid substitutions (K42E, K139R) in NR2 isolates of G-TF patients, which might affect protein structure. Also, a gene dosage effect as drug resistance co-variant/cause due to gene duplications or deletions of the hmp gene was tested. Results from dPCR revealed that...
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Nutrigenetic analysis of metabolic syndrome: the role of spontaneously hypertensive rat chromosome 4
Petrů, Karolína ; Šeda, Ondřej (advisor) ; Malínská, Hana (referee)
Metabolic syndrome (MetS) is a complex condition with a number of interacting genes, epigenetic and environmental factors underlying its pathogenesis. The analysis of genetic component of MetS showed that number of defining parameters of the syndrome is linked to regions of rat chromosome 4. In order to verify these quantitative trait loci (QTL), a double congenic strain was derived with parts of chromosome 4 of spontaneously hypertensive rat (SHR, an inbred MetS model) origin introgressed onto genomic background of congenic Brown Norway strain (BN-Lx). The aim of the proposed thesis is comprise detail genetic mapping of differential segments of the above mentioned double congenic strain BN-Lx.SHR4 and comparison of its metabolic profile under different dietary conditions with varying carbohydrate and fat content. Utilizing DNA sequence and gene expression comparisons, candidate genes or polymorphisms for the MetS aspects and potential nutrigenetic interactions will be identified. Key words: nutrigenetics, experimental models, metabolic syndrome, congenic strain, genotyping, rat
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Small ruminant lentiviruses - analysis of disease prevalence and distribution of SRLV genotypes in sheep and goat farms in the Czech Republic
VERNEROVÁ, Kateřina
Maedi-visna in sheep, and arthritis and encephalitis in goats, are globally widespread and progressive inflammatory diseases caused by retroviruses belonging to the small ruminant lentivirus (SRLV) group. They cause lifelong infections in affected animals, characterised by slow progression to overt disease and are always fatal. The aim of this study was to determine the prevalence of SRLV disease in the Czech Republic, to map the genotypic representation of SRLV using phylogenetic analysis, and to analyse TMEM154 as a selected candidate marker of SRLV resistance in sheep and goats. A total of 3 410 sheep and goat blood samples were collected from 21 flocks. The seroprevalence of maedi-visna in sheep was found to be 19.9% (556/2801), and the seroprevalence of arthritis and encephalitis in goats was 14.1% (86/609). All seropositive animals were tested by nested polymerase chain reaction (nPCR) for the presence of proviral DNA. Phylogenetic analysis identified the SRLV genotype in 77 sequences, of which 60 sheep and goat samples were genotype A and 17 sheep samples were genotype B. While all genotype B sequences were classified as subtype B2, the group of genotype A isolates showed higher variability and were related to subtypes A2 and A3. In addition, 40 seropositive and 50 seronegative sheep and goat samples were randomly selected to design a methodology for LAMP (loop-mediated isothermal amplification) diagnosis of SRLV in sheep and goats. Seronegativity was clearly confirmed by the LAMP method in all samples, and seropositivity was confirmed in 31 out of 40 cases in both sheep and goats. 605 sheep and 60 goat samples were randomly selected for TMEM154 genotyping. Most seropositive animals were heterozygous EK (61%), 58% were homozygous EE, and 45% were homozygous KK. In sheep, all 3 genotypes were identified, while all goats were homozygous EE.
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Výskyt a diverzita amphistomních motolic u skotu
VOGALOVÁ, Pavlína
The thesis deals with gastric woodlice of the family Paramphistomidae, which are common parasites of ruminants. Their immature stages can cause severe pathological changes in the host's digestive tract, and massive infection can lead to host death. Adult parasites cause infections of the rumen mucosa, resulting in lower production. The prevalence and diversity of these flukes is currently not systematically monitored. The aim of this study is to describe the occurrence and diversity of gastric flukes in cattle in the Czech Republic and Austria. The practical part consists of examination of dairy cattle faeces from different herds for the presence of eggs using standardised parasitological methods, optimization of a PCR method for direct detection of flukes from the faeces, genotyping of the flukes found, processing of the results using appropriate statistical methods, and comparison with published data.
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Role genu Socs3 v preimplantačním vývoji myších embryí
TOMÁNKOVÁ, Jana
The Socs3 gene is important for the postimplantation development of mouse embryos, but not much is known about its effect on preimplantation development. The aim of this study was to determine the effect of Socs3 gene in preimplantation development of mouse embryos, specifically on proliferation at E3.5 timepoint, at the time of seggregation of cell lineages trofoectoderm and inner cell mass.
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