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Integrated multi-omics analysis of chemical signaling in wild rodents
Matějková, Tereza ; Stopka, Pavel (advisor) ; Macholán, Miloš (referee) ; Bryja, Josef (referee)
Symbiotic bacteria living with the host in so-called microbiomes have been one of the significant pillars of all aspects of animal evolution, chemical communication included. However, the phenotype, genotype, and microbiome of laboratory animals kept for generations in sterile conditions changed from their wild ancestors leading to profound differences in the laboratory results and the reality of wild animals. To describe the chemical communication in neglected wild rodents, this thesis focuses on the body parts involved in chemical communication (i.e. mouth, vagina, and intestines) and are also inhabited by microbiomes that produce metabolites with the capability of transmitting chemical signals. Using next-generation sequencing and state-of-the-art proteome and metabolome chromatography-mass spectrometry, this thesis covers the analysis of changes in the microbiome, proteome, and metabolome of wild mice in the context of transferring the wild individuals into the captivity, cohousing wild, and laboratory animals and hormonal changes during the estrous cycles. Moreover, this thesis describes and discusses the differences and similarities in the microbiome, proteome, and metabolome on the level of different species (Apodemus sp.), subspecies (Mus musculus domesticus vs. musculus), and environment...
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Reproductive isolation barriers in the hybrid zone of the house mouse (Mus musculus)
Albrechtová, Jana ; Piálek, Jaroslav (advisor) ; Sedláček, František (referee) ; Reifová, Radka (referee)
Reproductive isolation occurring at the gamete level is called gametic isolation and almost always prevents gene flow between unrelated species and (to some extent) between closely related species or subspecies. The hybrid zone of the house mouse (HMHZ), which was formed by contact and interbreeding of two subspecies, the Western European house mouse (M. m. domesticus) and the Eastern European house mouse (M. m. musculus) provides a usefull model for the study of speciation processes involving gametic isolation. The probability of sperm competition within the female reproductive tract is high in the house mouse because high levels of sexual promiscuity (in 20˗40 % of all reproductive cycles) have been observed in this species. Thus, the reproductive isolation at gametic level may be determined both by the phenotypic characteristics of sperm (the ability to outcompete heterospecific sperm in the process of sperm- sperm competition) and by the preference of the sperm of conspecific males in the female reproductive tract (cryptic female choice). In my Ph.D. thesis I tested the degree of affinity of male and female gametes reciprocally between the both subspecies of M. musculus and the phylogenetically more distant species M. spretus, which is characterized by a higher degree of promiscuity. Although a...
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Genes of early meiotic prophase I of spermatogenesis in house mouse
Škaloudová, Eliška ; Trachtulec, Zdeněk (advisor) ; Forman, Martin (referee)
Meiosis is an essential cellular process that is necessary for gamete formation in all sexually reproducing organisms. This work is focused on the description of the genes of early stages of meiotic division in males of a mammalian model, the house mouse. The first part summarizes meiosis focusing on prophase I, which is longer than prophase II. Prophase I is divided into five stages, namely leptotene, zygotene, pachytene, diplotene, and diakinesis. Mouse spermatogenesis and its differences from oogenesis are also briefly described. The second part provides a list of genes encoding proteins required for initiation of meiotic division, pairing and synapses of chromosomes, and initiation of the catalysis of double-strand breaks. Double-strand breaks are repaired by homologous recombination, which may result in so-called crossing-over, the major source of genetic variability. The work deals with the early stage of homologous recombination and components required for this process. Localization of meiotic double-strand breaks in the genome is not random and is under the control of the Prdm9 gene, which seems to take multiple roles, such as the formation of new subspecies of the house mouse. Knowledge of the genes controlling the early stages of meiotic division is a prerequisite to understanding some of...
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Whole-genome analysis of the house mouse hybrid zone
Janoušek, Václav ; Munclinger, Pavel (advisor) ; Choleva, Lukáš (referee) ; Chan, Yingguang Frank (referee)
Hybrid zones provide a valuable opportunity to study the process of speciation in real time. Untested combinations of genes from diverging populations come to the contact here causing a breakdown of genetic interactions and giving rise to reproductive isolation. Two house mouse subspecies (Mus musculus musculus/Mus musculus domesticus) form a narrow zone of secondary contact across Central Europe which is thought to be maintained by a balance between selection against unfit hybrids and dispersion of individuals. During my PhD study my collaborators and I used an array of ~ 1400 SNP markers to study patterns of introgression on a genome-wide scale across two/three house mouse hybrid zone transects. Our aim was to identify the genomic regions putatively harboring genes which are involved in the reproductive isolation between the two subspecies, characterize their distribution in mouse genome and assess genomic features associated with them. We were able to confirm on a genome-wide scale the importance of the X chromosome in the evolution of reproductive isolation. This chromosome exhibited introgression corresponding to strong negative epistasis and the patterns were consistent between transects pointing out to a common basis of reproductive isolation playing a role in two transects. Contrary to the...
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The role of histone modifications and gene expression in mouse spermatogenesis
Křivánková, Klára ; Mihola, Ondřej (advisor) ; Jansa, Petr (referee)
The production of haploid sperm is a precondition for sexual reproduction of males. PRDM9 protein is a histone methyltransferase which localizes sites of meiotic recombination in many mammals. Mouse males of the C57BL/6J (B6) strain deficient for Prdm9 (Prdm9-/- ) are sterile, while Prdm9-/- males of PWD/Ph (PWD) strain have reduced sperm count. The comparison of the distribution of trimethylation of histone 3 on lysine 36 (H3K36me3) in genome of Prdm9-/- males of these two strains will help to determine the role of this epigenetic modification on meiotic recombination and fertility of Prdm9-/- males. The second part of this thesis is focused on transgenic males. Male offspring from the first generation of B6 female and PWD male crosses (B6PF1) have reduced fertility parameters due to incompatibility of Prdm9 alleles. The fertility parameters of B6PF1 hybrids carrying CHORI-34-289M8 or RP24-346I22 transgene are even lower. The candidate gene, which participates in the reduction of fertility of the transgenic B6PF1 hybrids, was determined as the proteasome subunit encoding gene Psmb1, because its relative transcription level best correlates with sperm count. The reason of lowered fertility thus might be a defect in proteasome assembly. The investigation of the fitness of transgenic animals is...
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Whole-genome analysis of the house mouse hybrid zone
Janoušek, Václav ; Munclinger, Pavel (advisor) ; Choleva, Lukáš (referee) ; Chan, Yingguang Frank (referee)
Hybrid zones provide a valuable opportunity to study the process of speciation in real time. Untested combinations of genes from diverging populations come to the contact here causing a breakdown of genetic interactions and giving rise to reproductive isolation. Two house mouse subspecies (Mus musculus musculus/Mus musculus domesticus) form a narrow zone of secondary contact across Central Europe which is thought to be maintained by a balance between selection against unfit hybrids and dispersion of individuals. During my PhD study my collaborators and I used an array of ~ 1400 SNP markers to study patterns of introgression on a genome-wide scale across two/three house mouse hybrid zone transects. Our aim was to identify the genomic regions putatively harboring genes which are involved in the reproductive isolation between the two subspecies, characterize their distribution in mouse genome and assess genomic features associated with them. We were able to confirm on a genome-wide scale the importance of the X chromosome in the evolution of reproductive isolation. This chromosome exhibited introgression corresponding to strong negative epistasis and the patterns were consistent between transects pointing out to a common basis of reproductive isolation playing a role in two transects. Contrary to the...
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Maping of genes modifying the subspecies-specific roles of the meiotic gene Prdm9
Škaloudová, Eliška ; Trachtulec, Zdeněk (advisor) ; Schierová, Michaela (referee)
The PRDM9 (PR domain containing 9) protein is an epigenetic factor that trimethylates lysine 4 of histone H3 and thereby determines the future meiotic double-strand breaks - sites important for proper segregation of homologous chromosomes. Males of the Mus musculus domesticus (Mmd) origin with homozygous deletion in Prdm9 (Prdm9-/- ) are sterile with a complete arrest in meiotic prophase I, in contrast to the same mutant males of the M. m. musculus (Mmm) subspecies. The aim of this diploma thesis was to identify the genomic loci responsible for the phenotypic difference of these Prdm9-/- males. The major research tool was a population of 182 Mmm x Mmd Prdm9-/- males. The mapping method of quantitative trait loci (QTLs) was based on relating the genotypes of single-nucleotide and microsatellite polymorphisms to the observed phenotypes. At least two QTLs on Chr X were identified. The Mmm alleles of these QTLs reduced fertility of Prdm9-/- males. Both QTLs were confirmed and narrowed down using two types of subconsomic strains. It was not possible to confirm other QTLs, particularly on autosomes. This QTL mapping is the first step towards the identification of genes that modify the resulting phenotype of Prdm9-/- animals. This identification should help designing studies of human infertility that...
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Genes of early meiotic prophase I of spermatogenesis in house mouse
Škaloudová, Eliška ; Trachtulec, Zdeněk (advisor) ; Forman, Martin (referee)
Meiosis is an essential cellular process that is necessary for gamete formation in all sexually reproducing organisms. This work is focused on the description of the genes of early stages of meiotic division in males of a mammalian model, the house mouse. The first part summarizes meiosis focusing on prophase I, which is longer than prophase II. Prophase I is divided into five stages, namely leptotene, zygotene, pachytene, diplotene, and diakinesis. Mouse spermatogenesis and its differences from oogenesis are also briefly described. The second part provides a list of genes encoding proteins required for initiation of meiotic division, pairing and synapses of chromosomes, and initiation of the catalysis of double-strand breaks. Double-strand breaks are repaired by homologous recombination, which may result in so-called crossing-over, the major source of genetic variability. The work deals with the early stage of homologous recombination and components required for this process. Localization of meiotic double-strand breaks in the genome is not random and is under the control of the Prdm9 gene, which seems to take multiple roles, such as the formation of new subspecies of the house mouse. Knowledge of the genes controlling the early stages of meiotic division is a prerequisite to understanding some of...
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Polymorphism of TLR2/TLR1 and TLR2/TLR6 heterodimers in wild-derived house mouse inbred strains
Bainová, Zuzana ; Vinkler, Michal (advisor) ; Hyršl, Pavel (referee)
Contrary to the classical mouse inbred strains with unnatural genetic variability, wild-derived strains offer a more suitable model for evolutionary immunology. Toll-like receptors (TLRs) belong to initial detectors of invading pathogens. Although TLRs recognise conserved structures they were shown to be polymorphic. This polymorphism is associated with various diseases. In my thesis, I describe variability of Tlr1, 2 and 6 in 24 inbred strains derived from two subspecies of house mouse (Mus m. musculus and M. m. domesticus). These Tlrs exhibit different levels in variability among the strains. In Tlr1 the polymorphic sites are spread along the whole exodomain. Tlr6 is quite conserved (a lower amount of substitutions located far from the binding region and with minor modifications in the amino acid residue properties). Tlr2, on the contrary, contains some substitutions with substantial alternations of residue properties that are located within or nearby the binding region and the subspecies differ at these sites. All alleles of M. m. domesticus and M. m. musculus, except for Tlr1 PWD, Tlr2 STAIL, are phylogenetically separated. The strains and the subspecies vary in the production of IL-1β, IL-12 a NO after stimulation by TLR1, 2 and 6 ligands. This trend is, however, presumably influenced by the effect of...
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Sex chromosomes in the house mouse hybrid zone
DUFKOVÁ, Petra
Understanding the genetic basis of reproductive isolation is the ultimate goal of the study of speciation. Here I present the results of a study of gene flow and its barriers at sex chromosome markers across the central European portion of the hybrid zone between two house mouse subspecies, Mus musculus musculus and M. m. domesticus. We identified strong introgression of Y musculus chromosome into the domesticus area accompanied by a perturbation of the census sex ratio. In addition, we detected stochastic effects that can distort results of hybrid zone studies. Finally, we confirmed a strong effect of sex chromosomes on reproductive isolation and hence their important role in the process of speciation.
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