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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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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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Introduction testing of mutation V600E in the BRAF gene in clinical laboratory
VÍTKOVÁ, Markéta
Nowadays, skin cancer belongs among very frequent tumor diseases. It has been proven that sun and skin cancer are maximally related, and thus it may affect everyone, however, ´light-type´ people having blonde or ginger-coloured hair, light skin and high numbers of freckles are much more likely to be affected. Skin tumors are most frequently localized in body areas that are exposed to sunshine in the long term, such as eyelids, nose, neck, shoulders and hands. The most frequent types of skin cancer are the following: Basaliom, Melanoma and Spinaliom. The aim of my bachelor thesis was to acquire theoretical knowledge about skin cancer, especially about the Malignant Melanoma. The Malignant Melanoma is, unlike the other epitelial tumors, such as Basaliom or Spinaliom, not characterized by local destructive growth, but by the danger of an early haematogenic or lymphogenic metastasis. The Malignant Melanoma often metastasizes into lymph nodes, however, distant metastases may also appear in skin, lungs, the brain and gastro-intestinal tract, mainly in the small intestine. The presence of mutations may be understood to be the biological cause of the Malignant Melanoma. One of the most significant and most described mutations (in connection to the Malignant Melanoma) is the BRAF gene V600E mutation, appearing in position No. 1799 in the area of codon No. 600. Codon GTG>GAG mutation leads to the exchange of valin for glutamic acid. Activating the mutated BRAF protein is a result of conformation changes within the protein structure. The mutated V600E BRAF cells are not subject to apoptosis and aging, the result of which is an incontrollable replicational potential of the cells. The mutated V600E BRAF Melanoma then escapes the organism´s immunity response. The aim of the practical part of my bachelor thesis was to acquire the basic molecularly biological methods in a genetic laboratory. Mainly isolating the genom DNA obtained from a buccal swab as well as peripheral blood, preparing and carriyng out a PCR reaction, preparing agarose gel, and detecting PCR products using gel electrophoresis. Mutation V600E within the BRAF gene examination was carried out via the PCR-ARMS method. The principle of this method relies in using four different primers able to detect both mutated and unmutated DNA sequence during one experiment. The methodology was taken over from Huang et al. (2013) and subsequently adapted to the needs of the laboratory.
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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Application of Data Engineering Technologies in Bioinformatics
SAIBOLD, Anna
Due to the huge amount of biological data, the various available data sources, and the diversity of their structure as well as content, data engineering technologies are required. They provide an important opportunity to support their exploitation. This thesis aims at applying several data engineering steps to a particular real-world data source to demonstrate the additional benefit with respect to utilization of the data by means of connecting to other data sources as well as querying and analyzing the data. Therefore, in the practical part of this thesis a continuous example showing several engineering steps is constructed, comprising the development of different schemata, the creation of a database as well as the mapping and integration of future heterogeneous data. Finally, processing queries against the engineered data source is compared to an online database search regarding different aspects like time, effort, and usability. As the example shows, an engineered database can have huge benefits over online search, especially for complex queries, processing data from several sources.
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Significance of detection of the ApoE gene and MTHFR gene polymorphisms for osteoporosis.
ŠILHOVÁ, Markéta
Osteoporosis is the sceletal metabolic disease characterized by changes of bone tissue and disfunction of mechanic bone resistance which can lead to numerous bone fractures. Osteoporosis is frequently diagnosed in patients older than 60 years, also advanced age patients are not an exception for this disease. The most frequently affected group of patients is postmenopausal women. Prevalence of osteoporosis still rises. Nowadays more than 200 millions of people suffer from osteoporosis and one million of patients from Czech republic. Osteoporosis have became a serious complication affecting not only medical but also an economic field. Based on these findings, osteoporosis should be considered as an important topic even from the perspective of genetic risk factors. The aim of my bachelor thesis is to write a specialized research focused on introduced topic, summarize accessible information about osteoporosis, including diagnosis and genetic predisposition. I have focused especially on genes ApoE and MTHFR677. ApoE plays an important role in sceletal homeostasis. The highest risk for osteoporosis development is the presence of alel 4 gene for alipoprotein E. Gen MTHFR677 is mostly associated with bone mineral density located in femoral neck. An experimental part of bachelor thesis was based on laboratory practice in molecular biology field inluding isolation of DNA from peripheral blood, PCR technique, detection of PCR products by gel agarose electrophoresis, analysis of ApoE gel by MyTaq Red DNA Polymerase kit and 2x PCRBIO HS Taq Mix, analysis of MTHFR677 gene by MyTaq Red DNA Polymerase kit. Analysis of ApoE gene is based on ARMS PCR method, on the other hand analysis of MTHFR677 is based on RFLP PCR method. I have performed the laboratory practice within the Laboratory of genetics GENLABS in České Budějovice.
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Studie antimikrobiálního účinku včelího jedu na druhy borelie z komplexu \kur{B. burgdorferi} sensu lato: izolace genu kódujícího antimikrobiální peptid melitin z jedové žlázy včely medonosné \kur{(Apis mellifera)}
DAVIDOVÁ, Marie
The incidence of tick borne diseases has drastically increased over the past few years. Control of tick borne pathogens, especially spirochetes from \kur{B. bugdorferi} sensu lato complex, is complicated due to a lack of vaccines against them. The emergence of bacterial strains to well established and widely used antibiotics has become a serious public health concern. Analysis of new classes of antimicrobial peptides became the subject of new investigation due to their efficacy against disease causing pathogens. Among possible candidates, melittin from honey bee venom is of particular interest. The aim of this work was to study the effect of whole bee venom on Lyme borreliosis spirochetes. The minimum concentration of the venom that possesed the inhibitory effect on borrelia growth was identified. The gene enconding melittin was isolated from bee venom gland and recombinant melittin was produced in bacterial expression system. The effect of recombinant melittin on live borrelia culture was studied.
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Gene order conservation in bacterial genomes
Martinková, Tereza ; Sedlář, Karel (referee) ; Maděránková, Denisa (advisor)
Theoretical part of the thesis deals with basic concepts such as bacterial genome, comparative genomics and mainly synteny blocks. Here is explained what synteny is and what is its importance. In the theoretical part, the GenBank format is also mentioned, its content and usage. The practical part is focused on searching similarities in DNA sequences of reference bacteria with selected bacteria, their sorting by means of greedy algorithm and visualization of similarities using phylogenetic tree.
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