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Influence of second and third generation sequencers on cgMLST analysis of closely-related bacterial strains.
Slavíček, David ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This bachelor thesis is about influence of sequncers of second and third generationon cgMLST analysis of bacterial genome. In the theoretical section were described selected sequencers of second and third generation and genome assembly principles. In the practical part were assembled six genomes of Klebsiella pneumoniae bacteria from University Hospital Brno. The genomes were sequenced each on two different sequencers, Illumina Miseq and Oxford Nanopore Technologies Minion. The genomes were assembled. Suitable genes were selected and insufficient quality genomes removed for the cgMLST analysis. The cgMLST analysis was performed and the results are shownin graphs.
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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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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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Examination of polymorphisms in the IFITM3 gene using sequences and their clinical significance for the course of viral diseases.
TROJÁKOVÁ, Simona
Interferon Induced Transmembrane Protein 3 is an anti-inflammatory cytokine that belongs to the group of interferon-stimulated genes. The topology of the IFITM3 gene was clarified by the analysis of electron paramagnetic and nuclear magnetic resonance. The protein encoded by this gene induces immunity against influenza A virus and other viral diseases. It also disturbs the homeostasis of intracelular cholesterol, inhibits the entry of viruses into the cytoplasm of the host cells and inactivates new enveloped viruses originating from an infected cell. IFITM proteins reduce virus replication by regulating the expression of viral protein and by reducing the infectivity of developing viruses. The analysis of the single-nucleotid polymorphisms in the IFITM3 gene is very significant to clarify the mechanism of the effect of the IFITM3 protein and its influence on the severity of the course of the viral diseases. The theoretical part deals with the description of Interferon Induced Transmembrane Proteins, particularly the description and function of the IFITM3 gene, including its polymorphisms. This gene is located on chromosome 11 and its size is approximately 18 Kb. The gene variability of the IFITM3 can fundamentally affect the course of influenza and other viral diseases. The practical part of the thesis focuses on the detection of polymorphisms rs12252, rs34481144 and rs1136853 in the IFITM3 gene using the PCR method and Sanger sequencing method. It was necessary to master some basic laboratory methods such as DNA isolation from primary samples, PCR method, preparation of the PCR product for sequencing, sequencing data analysis, processing of results and determination of specific genotypes in tested individuals.
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Detection of human adenoviruses from the respiratory samples from the patients of Motol University Hospital
NOVÁKOVÁ, Veronika
Human adenoviruses are world-wide pathogens causing endemic and epidemic outbre-aks of disease. Adenoviral infections are related with high morbidity and mortality especially among the paediatric allogeneic haematopoietic stem cell recipients. Presented work is comparing the commercial and in-house assay for detection of the adenoviruses to improve the diagnostics of these viruses in Motol University Hospital, especially among the immunocompromissed patients, in which is the rapid and precise detection highly important. Theoretical part of work presents the characteristics of adenoviruses, clinical symptoms and diseases of the adenoviral infection, their use in the experimental therapy. Practical part is aiming the screening of the respiratory tract samples with quantitative in-house test and comparing of the results with previously performed detection by commercial Anyplex TM II RV16 test. Detection of adenoviruses was performed in 1,881 samples from 1,420 patients with symptoms of respiratory tract infection by real-time PCR. In total, adenovirus was detected in 187 samples (9.9%) from 169 patients (11.9%). One hundred samples (53.5%) was positive by both methods, 26 (13.9%) with commercial detection only and 61 (32.6%) was positive only with in-house assay. Most frequently, adenoviruses were detected among the patients from Dept. of Paediatrics, Dept. of Paediatric Haematology and Oncology and from adult patients from 3rd Dept. of Surgery and Dept. of Anaestesiology, resuscitation and intensive medicine. In all positive samples, subsequent sequence analysis of hypervariable part of 1-6 hexon gene was performed and representative sequence for identification was obtained in 70 samples. Most frequently detected adenovirus genotypes were C2 (25.7 %), A31 (24.3 %), B3 (15.7 %) a C1 (11.4 %). From 26 samples positive by Anyplex TM II RV16, only 3 samples were identified (all as genotype B3). Contrary, among 61 positive samples detected only with in-house assay, 15 samples were identified as genotype A31 and 3 as AdV from group C. Our results shows the lower sensitivity of the commercial test in detection of adenoviru-ses.
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Výskyt laktózové intolerance v české populaci
CHÁNOVÁ, Jiřina
The aim of this diploma thesis is to summarize the current knowledge on the issue of very common gastrointestinal disorder - lactose intolerance. In the experimental part, the occurrence of genotypic frequencies in the MCM6 gene was screened. Specifically, the occurrence of two single nucleotide polymorphisms C/T-13910 and G/A-22018, which are associated with primary hypolactasia. A further aim of the work was to evaluate the possible association between lactose intolerance and irritable bowel syndrome.
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Influence of second and third generation sequencers on cgMLST analysis of closely-related bacterial strains.
Slavíček, David ; Sedlář, Karel (referee) ; Nykrýnová, Markéta (advisor)
This bachelor thesis is about influence of sequncers of second and third generationon cgMLST analysis of bacterial genome. In the theoretical section were described selected sequencers of second and third generation and genome assembly principles. In the practical part were assembled six genomes of Klebsiella pneumoniae bacteria from University Hospital Brno. The genomes were sequenced each on two different sequencers, Illumina Miseq and Oxford Nanopore Technologies Minion. The genomes were assembled. Suitable genes were selected and insufficient quality genomes removed for the cgMLST analysis. The cgMLST analysis was performed and the results are shownin graphs.
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Pregnancy proteins - molecular biological and biochemical analysis
Muravská, Alexandra ; Kalousová, Marta (advisor) ; Černá, Marie (referee) ; Průša, Richard (referee)
The aim of this thesis was to establish methods for selected PAPP-A (Pregnancy- Associated Plasma Protein A) gene polymorphisms analysis and to study genetic background of PAPP-A and biochemical background of PAPP-A and PlGF (Placental Growth Factor) in relation to risk pregnancy. Secondly, the aim was to establish method for two-dimensional (2D) electrophoresis of amniotic fluid. Methods for analysis of ten PAPP-A gene polymorphisms were established. These polymorphisms, PAPP-A and PlGF levels were studied in together 165 women in third trimester pregnancies complicated with threatening preterm labor (n=98), preeclampsia (n=35), IUGR (Intrauterine Growth Restriction) (n=34) and ICP (Intrahepatic Cholestasis of Pregnancy) (n=15). 114 healthy pregnant women served as controls. The method for 2D electrophoresis of amniotic fluid was established. Preeclamptic patients had significantly higher frequency of TT genotype of Cys327Cys (C/T) PAPP-A gene polymorphism compared to controls. Patients with ICP had increased serum levels of PAPP-A compared to controls, in patients with threatening preterm labor PAPP-A levels were rather decreased. PlGF levels did not differ from control group in patients with ICP and threatening preterm labor. Positive correlation was found between PAPP-A and PlGF in group of...
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