|
|
Development of Grey Partridge (Perdix perdix) microsatellite markers
Vaněčková, Dominika ; Munclinger, Pavel (advisor) ; Burri, Marta (referee)
The aim of this work was the construction of set of microsatellites for the Grey Partridge (Perdix perdix). I succeeded in isolation of seven new specific microsatellites. Another microsatellite markers were passed from close relative galliform species (Galliformes). On the whole I gained 18 microsatellite loci which were used for study of population charakteristics of three partridge populations from Stodůlky, Písecko and Milešín. The analysis showed conspicuous structuredness of these populations and surprisingly low values (less then 100) of their effective population sizes. Seven of the microsatellites were chosen for analysis of paternity. Indeed I found the evidence of extrapair paternity in this putatively monogamous bird. Finally I conclude, on the basis of sequenation of mitochondrial control region that our populations belong to the western linage of mitochondrial DNA.
|
|
|
Three-parent babies - new therapies of mitochondrial disorders
Helebrandtová, Veronika ; Pecinová, Alena (advisor) ; Ješina, Pavel (referee)
Mitochondria are essential parts of living cells, as they play a key role in cellular metabolism, especially in energy production. Due to their unique structure, the energy released during the oxidation of the substrates can be used to form the ATP. Mitochondria also contain their own DNA (mtDNA), which is maternally inherited and encodes catalytic subunits of oxidative phosphorylation complexes. Mitochondrial disorders of nuclear or mitochondrial origin, are common causes of inherited diseases and affect mainly the tissues with high energy requirements, such as heart or brain. Treatment of mitochondrial diseases is usually symptomatic and does not lead to complete recovery of the patient. As a result, new causal therapies, such as a gene therapy, are currently investigated. However, using this approach it is necessary to consider the origin of the mutation. Gene therapy of mitochondrial diseases of mtDNA origin is very complicated, therefore the new treatment strategy, mitochondrial replacement therapy, has been proposed. The principle of this technique is to prevent the transmission of mutated mtDNA from mother to offspring by transferring the nuclear genome of mother with mitochondrial disorder into donor's denucleated oocyte with healthy mitochondria. In this way, the child has genetic...
|
|
|
Conservation genetics of the grey wolf in Central Europe
Valentová, Kamila Anna ; Hulva, Pavel (advisor) ; Galov, Ana (referee)
Conservation genetics of the grey wolf in Czech Republic and adjacent regions is studied in the present thesis. Analyses of twenty-one microsatellite loci, one sex-determining amelogenin gene and mitochodrial control region were used to verify species determination, identify individuals and estimate relationships between them, analyse population structure and estimate demographic trends based on samples collected between 2014 and 2021. Genetic detection of red fox and dog samples incorrectly assigned to wolves illustrates the hurdles of field monitoring of grey wolf. Direct evidence for the occurrence of F1 hybrids was not found. Wolves from Bohemia showed lower values of allelic richness in comparison to the ones from Western Carpathians, probably as a consequence of recent expansion. Geographic distances between detection sites of identical individuals were relatively small or moderate in this study, suggesting regular movements of animals within their home ranges. Only two long-distance dispersal events exceeding 300 km were detected. Results of parental analysis provided evidence of pack distribution within the studied area. Most relationships were detected between wolves in the northern region of Czech Republic where the first recolonizing wolf pack in 2014 was registered. Within the studied...
|
|
|
Population genetics of Pipistrellus pipistrellus species complex hibernacula
Habalová, Kateřina ; Hulva, Pavel (advisor) ; Kaňuch, Peter (referee)
This thesis deals with two cryptic pipistrelle bat species, common pipistrelle (Pipistrellus pipistrellus) and soprano pipistrelle (Pipistrellus pygmaeus) living in sympatry in continental Europe. Although both species are abundant during summer in Europe, they spent winter in mass hibernacula and there is only limited knowledge about this period. In total, 233 individuals from four mass hibernacula were sampled in Central Europe and Romania. The species composition and population variability in winter hibernacula was examined by using the tools of population genetics (analysis of mitochondrial sequences and nuclear microsatellites). Two hibernacula with exclusive or partial mass representation of soprano pipistrelle were genetically confirmed for the first time. No cytonuclear conflict neither admixed nuclear genotype was detected, that means that early stage of hybridization between both species was not revealed. Similar genetic structure in both genetic markers indicate, that swarming and hibernating populations are substantially overlapping. Compared to the P. pygmaeus, higher genetic variability was found in P. pipistrellus populations, even though genetic variability is relatively low compared to other species. It can be caused by strong gene flow, in the case of P. pygmaeus it may be caused...
|
|
|
Synonymous codon usage bias in mitochondrial genomes
Urbanová, Hedvika ; Cicková, Pavlína (referee) ; Maděránková, Denisa (advisor)
This Bachelors thesis deals with synonymous codon usage bias in mitochondrial genomes. This thesis covers basic terms of bioinformatics and genetics. Codon usage bias is introduced together with parameters that characterize it. Practical part of the thesis is dealing with programs that are designed to calculate parameters of codon usage bias. Programs that are described in this thesis are relative synonymous codon usage, relative adaptation index, codon adaptation index, homozygosity of codons, and effective number of codons. Synonymous codon usage bias in mitochondrial genome of Homo sapiens is analysed.
|
|
|
Deletions in human mitochondrial DNA and causes of their formation
Zdobinský, Tomáš ; Tesařová, Markéta (advisor) ; Kazantsev, Dmitry (referee)
Mitochondria are organelles of eukaryotic cells that primarily provide energy metabolism, but also participate in metabolic processes such as biosynthesis of amino acids, heme groups, Fe-S clusters etc. Mitochondrial disorders represent heterogeneous group of diseases which can occur in both child and adult life. They affect various tissues and organs in different ways, most often manifesting themselves as disorders of nervous system, skeletal muscle, liver, kidneys or endocrine system. Mitochondrial DNA deletions contribute to pathogenesis of many of those diseases and they are a symptom of several defined syndromes. They most likely arise as a result of replication stalling resulting in a double strand break of DNA. This can be caused primarily by pathogenic changes in replication apparatus and nucleotide metabolism proteins. The aim of this work is to summarize the knowledge about mitochondria and structure and replication of their genome, but also to create a summary of the most important proteins whose mutation leads to mitochondrial diseases accompanied by deletions in mtDNA and to outline the mechanism by which they arise.
|
|
|
Sequence diversity of mtDNA and genetic structure of eastern part of the African Sahel
Tlačbabová, Klára ; Černý, Viktor (advisor) ; Munclinger, Pavel (referee)
Eastern part of the African Sahel, connecting sub-Saharan Africa with North and East Africa, play an important role as a bidirectional corridor for vertically and horizontally migrations of populations. It is the strategic region to study human genetic diversity due to the presence of ethnically, linguistically, culturally and geographically diversity. This work is focused on the analysis of HVS-I and HVS-II segments of mtDNA. The work provides new information about genetic structure and migration activity of this region by analysis twelve populations belonging to three African linguistic families and different subsistent strategies. Analysis of mtDNA revealed the higher diversity of the populations of east Sudan and Horn of Africa, which is connected with the spreading of populations along the Nile River. It seems, that in this region linguistic factors have bigger impact on genetic diversity then the geografic ones. The opposite situation is observed in populations of Chad, where populations with similiar geografic location and different linguistic affilation revealed low genetic differentiation. The intra-population analysis shows the significant influence of genetic drift on the pastoralists living on the Red Sea Coast - Beja and Rashaida. In Beja is probably due to decrease of size of...
|
|
|
Mutation and substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis?
Röslein, Jan ; Janko, Karel (advisor) ; Rothová, Olga (referee)
Univerzita Karlova v Praze Přírodovědecká fakulta Studijní program: Molekulární biologie, genetika a virologie Bc. Jan Röslein Mutační a substituční tempo u sexuálních a klonáních forem: možný klíč k vysvětlení persistence sexu u modelové skupiny sekavců Mutation AND substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis? Typ závěrečné práce Diplomová Vedoucí závěrečné práce: Mgr. Karel Janko, Ph.D. Praha, 2015 Velký dík náleží mému školiteli Mgr. Karlu Jankovi, Ph.D. za velmi nápomocné, direktivní vedení práce. Též bych rád poděkoval panu Mgr. Janu Pačesovi, Ph.D. za více než vzdělávací rozměr v oblasti bioinformatické analýzy a Mgr. Ladislavu Pekárikovi, Ph.D., Mgr. Janu Kočímu za pomoc při analýze vybraných kapitol. Také bych rád poděkoval rodině za podporu. Všem participantům na této diplomové práci se hluboce omlouvám za způsobenou psychickou újmu. Prohlášení: Prohlašuji, že jsem závěrečnou práci zpracoval/a samostatně a že jsem uvedl/a všechny použité informační zdroje a literaturu. Tato práce ani její podstatná část nebyla předložena k získání jiného nebo stejného akademického titulu. V Praze dne 12. 8. 2015 Podpis: Abstrakt Klíčová slova: Abstract Key words: Obsah 1...
|
|
|
Mutation and substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis?
Röslein, Jan ; Janko, Karel (advisor) ; Rothová, Olga (referee) ; Reifová, Radka (referee)
TITLE: Mutation and substitution rates in sexual and asexual forms: a clue to the persistence of sex in a model group of Cobitis? AUTOR: Jan Röslein DEPARTMENT: Ústav živočišné fyziologie a genetiky AVČR, v.v.i. SUPERVISOR: Mgr. Karel Janko, Ph.D. ABSTRACT: Subject of this thesis is to test several hypotheses about the evolution of asexual reproduction in model group of fish family Cobitis and its mutual competition among sexual and asexual forms, which touches one of the oldest unresolved issues of biology. Specifically, the work deals with the accumulation of non-synonymous mutations, which accelerated accumulation in the genome of clonal lineages theoretically leads to increased extinction compared with sexually reproducing populations (so-called. The theory of Muller's ratchet and Kondrashov's hatchet). This thesis is based on a normalized cDNA sequencing data from oocytes and liver tissue, which has served as a base matrix (generated based on non-normalized cDNA data) for transcriptome sequencing (RNAseq). Consequently, the RNAseq data have served as validation for acquired polymorphisms, detection of differential expression of allele- specific expression (ASE) hybrid biotypes. This diploma thesis balances among the edges of vast spectrum of hypotheses regarding the evolution of the genus hybrid...
|
|
|
Mitogenomic phylogeography and adaptive evolution of the bank vole Clethrionomys glareolus
Filipi, Karolína ; Kotlík, Petr (advisor) ; Munclinger, Pavel (referee)
This thesis is a part of the project aimed at sequencing the genome and transcriptome of the bank vole (Clethrionomys glareolus). The role of natural selection in the evolution of mitochondrial DNA (mtDNA) has been subject to much discussion; while some studies did not provide evidence that selection affected the phylogeography of the studied species, other considered adaptive evolution important. The bank vole is the key model we use to study the adaptation to climate change. As with other species, the phylogeography of the bank vole has been based on the variation of a small part of mtDNA. The goal of the thesis was to sequence the entire mitochondrial genome for representatives of all main mtDNA lineages of the bank vole using the Sanger and Illumina technologies, and to assess the role of selection and adaptation in the evolution and phylogeography of this species. The adaptive evolution in mtDNA probably was not the main driving force during the postlacial colonization of Europe. However, signatures of adaptive evolution have been found - an amino acid change with possible functional consequences in one gene and an excess of radical changes in physical- chemical properties of amino acids in populations at the latitudinal (northern and southern) extremes of the bank vole distribution. Key...
|
guest ::
