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Dynamic metabolomic prediction based on genetic variation for Hordeum vulgare
Nemčeková, P. ; Schwarzerová, J.
Hordeum vulgare, like many other crops, suffers from the reduction of genetic diversity caused by climate changes. Therefore, it is necessary to improve the performance of its breeding. Nowadays, the area of interest in current research focuses on indirect selection methods based on computational prediction modeling. This study deals with dynamic metabolomic prediction based on genomic data consisting of 33,005 single nucleotide polymorphisms. Metabolomic data include 128 metabolites belonging to 25 Halle exotic barley families. The main goal of this study is creating dynamic metabolomic predictions using different approaches chosen upon various publications. Our created models will be helpful for the prediction of phenotype or for revealing important traits of Hordeum vulgare.
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Metabolite Genome-Wide Association Studies Of Arabidopsis Thaliana
Schwarzerová, Jana
Current research based on the edge of bioinformatics and ecology engineering has hugepotential due to combination of laboratory analyses and advanced bioinformatics algorithms.The paper deals with a combination of GC-MS and LC-MS based metabolomic analysis for identificationand quantitation of metabolites in environmental perturbations with advanced bioinformaticsapproach of metabolite genome-wide association studies (mGWAS). This complex view is appliedto Arabidopsis thaliana. The main goal is to obtain genetic predictions focused on A. thalianaunder different environmental conditions. Currently, important ecological issues such as climatechange, pollution etc. have impact on the change of environment. It has a great effect on plantswhich serves as producers of oxygen or food. While simple observation reveals only a phenotypechange, changes in genotypes of organisms can be captured using mGWAS and further utilized inindustrial ecology and biotechnology.
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Frequency of occurrence of selected single nucleotide polymorphisms of CYP2C8 and MDR1 in the Czech population and their influence on the effect of amiodarone
Pechandová, Kristina ; Perlík, František (advisor) ; Král, Jiří (referee) ; Anzenbacher, Pavel (referee)
Frekvence výskytu vybraných bodových polymorfismů CYP2C8 a MDR1 v české populaci a jejich vliv na působení amiodaronu Úvod: Variabilita lékové odpovědi je někdy podmíněna genetickými rozdíly v metabolismu a transportu léčiv. Interindividuální rozdíly jsou často způsobeny polymorfismy, které ovlivňují biotransformační aktivitu enzymů a expresi transportérů. V disertační práci jsme věnovali pozornost cytochromu P450 izoenzymu CYP2C8 a MDR1. Nejprve jsme popsali frekvenci výskytu vybraných variantních alel CYP2C8*2, CYP2C8*3 (2 substituce v exonu 3 a 8, CYP2C8*3G416A a CYP2C8*3A1196G), CYP2C8*4, CYP2C8 P404A u zdravé české populace a variantních alel MDR1 v exonech: 26 C3435T, 21 G2677A/T, 12 C1236T a 17 T-76A. Následně jsme sledovali vliv těchto polymorfismů na působení amiodaronu u vybraného souboru pacientů. Metody: Genotyp MDR1 a CYP2C8 jsme stanovili pomocí PCR-RFLP za využití specifických restrikčních enzymů a primerů. Frekvence genotypů MDR1jsme určili u 189 zdravých dobrovolníků a CYP2C8 u 161 zdravých osob. Do sledování jsme dále zařadili 63 pacientů užívajících amiodaron déle než dva měsíce. Jejich léčbu jsme posuzovali ze záznamů lékařské dokumentace, s využitím standardních biochemických a hematologických vyšetření a záznamů EKG. Koncentrace amiodaronu a jeho metabolitu N-...
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Frequency of selected genetic polymorphisms of cytochrome P450 in the Czech population and the influence of CYP2C9 genotype on the hypolipidemic effect of fluvastatin
Buzková, Helena ; Perlík, František (advisor) ; Bultas, Jan (referee) ; Mičuda, Stanislav (referee)
55 Abstract Frequency of selected genetic polymorphisms of cytochrome P450 in the Czech population and the influence of CYP2C9 genotype on the hypolipidemic effect of fluvastatin Introduction: One of the main factors of genetically determined variability in response of humans to administered drugs are differences in catalytic activity of metabolizing enzymes, which are caused mainly by genetic polymorphisms in cytochrom P450 family enzymes. This thesis consists of two parts and it is presented as a commentary to the original papers. The first aim was to investigate the frequency of functionally important variant alleles of three main isoenzymes of cytochrome P450 gene: CYP2D6, CYP2C9, CYP2C19, throughout the Czech population, predict the prevalence of poor metabolizer phenotypes, and then to compare the results to the data from other populations. Secondly, we analysed the correlation between the CYP2C9 genotype and cholesterol-lowering effect of fluvastatin in human hypercholesterolemic patients. Methods: Genotypes were determined by PCR-RFLP. The presence of alleles CYP2D6*1, *6, *5, *4, *3, and gene duplication was analysed in 233 healthy volunteers, CYP2C9*1, *2 and*3 in 254 subjects and CYP2C19*1, *2 and *2 in 218 subjects. Eighty seven patients on fluvastatin therapy, and 48 patients on monotherapy...
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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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Study of genetic and infectious risk factors in the pathogenesis of obesity in Czech adolescents.
Elblová, Lenka
4 Abstract The prevalence of obesity and its related cardiometabolic complications in children remains high across the world. Obesity is a multifactorial disease caused by interaction between genes and environmental factors. Genome-wide association studies have discovered several single nucleotide polymorphisms associated with obesity. A causal role of infection in the pathogenesis of obesity has also been considered, particularly the role of adenovirus 36 (Adv36). The aim of the Ph.D. thesis was to investigate the associations of obesity susceptibility loci (TMEM18, SH2B1, KCTD15, PCSK1, BDNF, SEC16B, MC4R, FTO) and Adv36 infection with obesity-related characteristics and complications in the Czech adolescent population. The results are described in eight publications, of which six are original papers and two are reviews. Studies were performed on a cohort of Czech adolescents recruited either from the general population (1,533 individuals from the epidemiological study) and from in-patient or outpatient weight management clinics (562 overweight/obese individuals underwent an intervention). The results demonstrated an association of TMEM18, SEC16B and FTO gene variants with obesity. Some variants of the genes involved in hypothalamic regulation of energy homeostasis − MC4R, BDNF, PCSK1 − were related to...
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Study of genetic and infectious risk factors in the pathogenesis of obesity in Czech adolescents.
Elblová, Lenka
4 Abstract The prevalence of obesity and its related cardiometabolic complications in children remains high across the world. Obesity is a multifactorial disease caused by interaction between genes and environmental factors. Genome-wide association studies have discovered several single nucleotide polymorphisms associated with obesity. A causal role of infection in the pathogenesis of obesity has also been considered, particularly the role of adenovirus 36 (Adv36). The aim of the Ph.D. thesis was to investigate the associations of obesity susceptibility loci (TMEM18, SH2B1, KCTD15, PCSK1, BDNF, SEC16B, MC4R, FTO) and Adv36 infection with obesity-related characteristics and complications in the Czech adolescent population. The results are described in eight publications, of which six are original papers and two are reviews. Studies were performed on a cohort of Czech adolescents recruited either from the general population (1,533 individuals from the epidemiological study) and from in-patient or outpatient weight management clinics (562 overweight/obese individuals underwent an intervention). The results demonstrated an association of TMEM18, SEC16B and FTO gene variants with obesity. Some variants of the genes involved in hypothalamic regulation of energy homeostasis − MC4R, BDNF, PCSK1 − were related to...
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