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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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Conservation genetics of Galápagos mockingbirds: from immune genes to genomes
VLČEK, Jakub
In this thesis I have dealt with the population genetic processes of mockingbirds in the Galápagos Islands ( Mimus ) in relation to the limited island area, from the perspective of two types of immune genes and the genome-wide approach. The thesis starts with an introduction to population genetic concepts relevant to conservation genetics followed by description of immune genes: the major histocompatibility complex (MHC) and the Toll-like receptors (TLR). In the final part of the introduction, I address how genetic drift, selection and inbreeding shape genome-wide genetic patterns in small populations. The introduction is followed by four chapters, beginning with an examination of MHCII polymorphism in populations of mockingbirds in the Galápagos Islands. The study of the relationship between MHCII and the abundance of ectoparasites is the content of the second chapter. The third chapter shows how polymorphism of TLRs is shaped by interaction of genetic drift and natural selection. The last chapter deals with the effects of limited island size on inbreeding and genetic load, supported by inferences of the past demography of mockingbirds. The thesis concludes with a summary of the results and their potential implications in the field of conservation genetics.
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Bottleneck and selection effects on MHC genes variability in relic and newly formed Eurasian beaver populations
Náhlovský, Jan ; Munclinger, Pavel (advisor) ; Bryja, Josef (referee)
MHC glycoproteins are an essential part of adaptive immunity and may also play a role in mate choice. In addition, MHC genes are the most variable of all known genes. For these reasons, they have been intensively studied for several last decades. However, research is complicated due to extreme variability and frequent duplications. The Eurasian beaver seems to serve as an interesting model. It underwent a dramatic bottleneck culminating in the end of 19th century, when only about 1,200 individuals survived in several isolated relic populations. Thanks to numerous reintroductions, beavers of various origin meet in newly established populations. However, knowledge of beaver MHC was very limited. Only a single MHC gene has been investigated in a detail, and some relic populations were not sampled. Utilising additional relic populations and additional MHC locus, I verified a significant reduction of the variability of beaver MHC genes and also found signs of selection in the past. Then I sequenced MHC loci in two newly formed populations. I confirmed the ongoing selection by the disruption of cytonuclear equilibrium and the advantage of divergent alleles. We therefore can have a unique insight into the several periods of the history of beaver populations: In the past, MHC diversity was shaped by a...
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Effect of hormonal contraception use during relationship formation on subsequent relationship satisfaction
Fiurašková, Kateřina ; Havlíček, Jan (advisor) ; Pastor, Zlatko (referee)
Results of previous studies testing the influence of oral contraceptives on relationship satisfaction have produced mixed results. These discrepancies might be explained by the "Congruency hypothesis", which predicts that relationship satisfaction is determined by the congruency (or non-congruency) between current use of oral contraceptives and their use during relationship formation. This is because oral contraceptives appear to alter women's mate preferences, so that attraction to their partner may have changed in non-congruent women. Indeed, previous studies have shown that women in a non-congruent state were less sexually satisfied with their partner, even though they were more generally satisfied in the non- sexual aspects of the relationship. The aim of our study was to test the congruency hypothesis on two groups of couples (couples attending the Center of Assisted Reproduction, and a comparison group of pregnant women and their partners; note that in neither group were women currently using oral contraception). Based on previous studies, we expected that women who used oral contraceptives at the time of relationship formation would report lower sexual satisfaction with their partner than women who were non-users during relationship formation. The study involved a total of 660 couples from...
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Trans-species polymorphism in immune genes at wildlife animals
Těšický, Martin ; Vinkler, Michal (advisor) ; Matiašovic, Ján (referee)
Trans-species polymorphism (TSP) is described as the occurrence of identical or similar alleles in related species, excluding cases where the similarity arose by convergence. In TSP the alleles are inherited from ancestor to the descendant species. Neutral TSP is frequent in closely related newly diverged species and it gradually disappears. Considering evolution of immune system and host- pathogen interaction, balanced long-lasted TSP is much more important. Balanced TSP in immune- related genes is maintained by the mechanism of balancing selection and commonly persists for millions of years. In my thesis I map the contemporary knowledge on TSP in immune-related genes, focusing mainly on wild animals. The chief emphasis is given to evolutionary mechanisms influencing the width and age of TSP, distinguishing TSP from other TSP-like evolutionary patterns and methodical difficulties with the assignment of TSP. Presently, most articles dealing with TSP concentrate only on genotyping the Major histocompatibility loci (MHC I and MHC II), especially in the peptide binding region. Our knowledge concerning other immune genes with putative TSP is, therefore, insufficient. Most importantly, this is true for innate immunity genes. More effort should be given to comparative large-scale well-sampled studies...
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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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Variability of MHC class II \recke{beta} gene in Galápagos mockingbirds
VLČEK, Jakub
Understanding the dynamics of functional genetic variability in small populations can have important implications in their conservation. I screened the variation of MHC II gene in Galapagos mockingbirds to evaluate the evolutionary forces that shaped the genetic variation. I found out that genetic drift affected the MHC variation together with a specific form of natural selection. Although the MHC is supposed to be under a pathogen-mediated selection I found no evidence for this theory in the mockingbird study system.
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