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Application of Hyb-Seq method for reconstruction of reticulate infrageneric phylogeny: example from polyploid genus Curcuma L. (Zingiberaceae)
Skopalíková, Jana ; Fér, Tomáš (advisor) ; Krak, Karol (referee)
This master thesis focuses on the phylogeny of hybridogenous and polyploid genus Curcuma from family Zingiberaceae using Next-Generation Sequencing data from hundreds to thousands nuclear loci. This approach seems to be better than widely used cpDNA and ITS sequencing especially in the case of hybridogenous and polyploid groups. Data for phylogeny reconstruction were generated using Hybridization-based sequencing (Hyb-Seq) method which combines target enrichment and genome skimming strategies. Data analysis was performed primarily using pipeline HybPhyloMaker especially created for Hyb-Seq data analysis. Twenty-seven species from the genus Curcuma and three outgroup species were sequenced in this work. Phylogenetic trees based on all 1 154 and 811 selected nuclear low- copy genes show high support values of all nodes which is in contrast to plastome and rDNA phylogeny with lower support values in some nodes and incongruences in topology compared to low-copy genes phylogeny. Phylogenetic networks inferred from low-copy genes, lineage movement analysis and monophyly tests agree with published hypotheses of interlineage hybrid origin of three species - C. vamana, C. myanmarensis and C. roscoeana. These analyzes show likely hybrid origin of C. candida too with parents from the group Curcuma I and basal...
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Variation and interspecific hybridization of Elymus repens and E. hispidus
Bartošová, Romana ; Urfus, Tomáš (advisor) ; Chrtek, Jindřich (referee)
Family Poaceae is one of the most derived groups of monocots. Major mechanisms of grasses evolution and particularly of tribe Triticeae and genus Elymus are polyploidisation and hybridisation. Presented diploma thesis assessed frequency and direction of hybridisation between Elymus hispidus and E. repens in Central Europe. Thesis also evaluated evolutionary importance (significantly higher ratio of hybridisation and polyploidisation) of hybrid swarm in Nature Reserve Čertoryje (Bílé Karpaty Mountains/the White Carpathians, the Czech Republic). Putative hybridizing populations were 14,4 % of sampled localities, i.e. direct presence hybrids (7,9 %) or both parental species (8,4 %). Aneuploids and higher polyploids were found exclusively in Čertoryje hybrid swarm, except one putative DNA nonaploid plant. The genome in situ hybridisation confirmed and improved knowledge of particular species/cytotypes chromosome counts and further specified their genome composition. GISH newly characterized genome composition of interspecific hybrids and higher allopolyploids and revealed their heterogeneous origin. Flow cytometry revealed continuum of absolute genome sizes among parental species and their hybrid. The continuum was rather asymmetric in direction towards E. hispidus. Model hybrid swarm Čertoryje produce...
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Variability in health state of mice in Mus musculus musculus and Mus musculus domesticus hybrid zone
Bílková, Barbora ; Vinkler, Michal (advisor) ; Vetešníková Šimková, Andrea (referee)
House mouse hybrid zone is a complex of subspecies Mus musculus musculus, Mus musculus domesticus and their hybrids. This hybrid zone is considered as a tension zone, maintained by balance between dispersion of individuals towards the zone center and negative selection against the hybrids. Decreased anti-parasite resistance could be one of selective factors which maintain the hybrid zone. In this thesis, I use hematological methods and skin-swelling test to compare variability in mouse health state within the house mouse hybrid zone. The skin-swelling test is a method measuring pro-inflammatory immune responsiveness. Since the commonly adopted method to perform this test does not allow clear interpretation of the test results, in this thesis I also aim to optimise the test protoco . I found that utilization of concanavalin A (ConA) is more suitable in mice than application of the commonly used phytohemaglutinin (PHA). Assessment of health state of mice by both hematological methods and skin-swelling test consistently indicates increased ability of anti-parasitic resistance in the subspecies M. m. musculus compared to subspecies M. m. domesticus. Hematological examination further shows better health state of hybrid individuals compared to parental subspecies. Our results support hybrid resistance hypothesis....
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Neutral genetic variability and structure in chamois populations in Slovakia
Hájková, Andrea ; Zima, Jan (advisor) ; Kotlík, Petr (referee)
The Tatra chamois (Rupicapra rupicapra tatrica), an endemic mountain ungulate, occurs in the High Tatra Mts. (northern Slovakia and southern Poland). In the second part of the 20th century several chamois introductions occurred in Slovakia: Tatra chamois (from the High Tatra Mts.) were introduced into the Low Tatra Mts., while Alpine chamois (R. r. rupicapra) into the Veľká Fatra and Slovenský raj Mts. The High Tatra Mts. population underwent several population declines (bottlenecks) and all other Slovak populations were founded from only a few individuals (founder effect). Moreover, because the Low Tatra, Veľká Fatra and Slovenský raj are neighbouring mountain ranges, there is a potential risk of migration and hybridisation between the subspecies. Using 18 microsatellite loci, we studied neutral genetic variability, structure and potential hybridisation in chamois populations in Slovakia. The study is based on 193 samples: 95 tissue and 5 blood samples, and 88 faecal and 5 hair samples. Low genetic variability was found in all populations, the lowest one in High Tatra Mts. population. High values of fixation index, the number of private alleles, and factorial correspondence analysis indicated strong differentiation between the studied populations. Bayesian clustering divided Slovak chamois...
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The importance of predisposition examination of late Alzheimer´s disease using methods of molecular biology
KOPAČKOVÁ, Michaela
Alzheimer's disease is the most common type of dementia. It affects up to 70% of cases from approximately 38 million people worldwide suffering from some type of dementia. Alzheimer's disease usually affects patients over 65 years of age, however, there are exceptions. It is presumed that the number of people with Alzheimer's disease will grow constantly in the future too. Its etiopathogenesis is not yet fully understood, that is why it is important to investigate dementia further, whether in terms of specific environmental and genetic risk factors, or in view of the economic burden for the society. The presented bachelor's thesis summarises findings about Alzheimer's disease, its neurobiology, etiology, diagnostics and genetic predispositions, in particular the ApoE, APP, PSEN1 and PSEN2 genes. The presence of epsilon 4 gene allele for apolipoprotein E provably contributes to the increased risk of the late form of Alzheimer's disease. On the contrary, mutation in APP, PSEN1 and PSEN2 genes are connected with Alzheimer's disease with the early onset of the disease, before 65 years of age. The objective in the experimental part was to manage the practical isolation of DNA from peripheral blood and buccal swab, preparation and execution of PCR reaction, detection of PCR products by gel electrophoresis and independent examination of ApoE gene by a certified CVD StripAssay Kit from ViennaLab company (PentaGen). The work also includes the optimisation of another molecular genetic method for the detection of variant alleles of ApoE gene. This method was carried out by a certified DiaPlexQTM ApoE Kit from SolGent Co., Ltd. The principle of detection in this case is based on real-time PCR.
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Microarray Data Analysis
Vogel, Ivan ; Smrž, Pavel (referee) ; Šilhavá, Jana (advisor)
The aim of this bachelor thesis is to describe the DNA microarray technology. Several analytical algorithms are discussed. It describes closely the clustering methods, especially several hierarchical clustering modifications. It gives a summary of available commercial and uncommercial software for microarray analysis. The thesis describes own implementation design of hierarchical methods. At the end, results are compared with similar uncommercial software.
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Post - conceptual Approaches in the Contemporary Czech Painting
Dub, Petr ; David,, Jiří (referee) ; Havlík, Vladimír (referee) ; Zálešák, Jan (referee) ; Stratil, Václav (advisor)
The dissertation thesis entitled Selected Post-conceptual Approaches in the Contemporary Czech Painting reflects the author’s expressions of the youngest artists’ generation working with the conceptual forms in the painting medium after 1996. The aim of the dissertation is to outline the conflict and overlapping of the conceptualism and painting. Apart from the development of conceptual art, the reference framework of the submitted thesis also comprises the post-modern turn in visual arts associated with a global change in its social status during the second half of the 20th and at the beginning of 21st century. The development of the domestic artistic scene and particular approaches are presented on the basis of a representative selection of the most distinctive tendencies and significant authors, being compared with the work of foreign artists. The text interprets the key theoretical treatises, reviewed responses and artists’ statements covering the domain of “contemporary painting to conceptual art”.
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Living in Intensive Urban Structures
Zadražilová, Miroslava ; Urbášková, Hana (referee) ; Šimeček, Pavel (referee) ; Vitková, Lubica (referee) ; Menšíková, Naděžda (advisor)
As a result of changes in the society, such as the increasing mobility, increasing spatial demandindgness of inhabitants and the onset of digital technologies, the architects and urbanists have been searching for new ways of urban housing developments. One of these ways is densification, i.e. an intensive use of the urban space. An intensive urban structure uses up the potential of a place to its maximum, solves several issues simultaneously and is a functional hybrid, the home of potential suburbanizers and a place of social contacts. It comes from the efforts to solve the particular issue of an over-populated, collapsing city. The aim of the thesis is to show contemporary approaches to the issue of intensive urban structures and to map out both the built and unbuilt projects. The thesis creates a system of their categorization and taxonomy. There is always a mixture of functions in play from the functional perspective. One can distinguish five categories according to the spacial conception. These categories are as follows: multiplicity, porousness, hybridity, connectivity and verticality. The public and semi-public spaces thus move to the higher levels of the city, into the city level, urban balcony or the hybrid landscape. The built projects usually tend to be impulses, in relation to the original city, to develop and revitalize the devastated city areas, brownfields, even urban sprawls. Based on the findings of this thesis, diploma and pre-diploma project assignments have been created at the architecture department at FAST VUT in Brno and the approaches to the issue have been tested in the pedagogical process. The survey in the second part of the thesis looks for the answer to the question of whether the potential inhabitants of an intensive urban structure exist, and who these people might be.
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The Municipal Baths
Vrbka, Jan ; Kyselka, Mojmír (referee) ; Makovský, Zdeněk (advisor)
Are municipal bath built next to Voronez Hotel able to compete with other such facilities? The key is to create a specific atmosphere. The bath steeps from the ground to offer views over city. Another part of the strategy is a presence of relative functions in the building – you can meet many activities, which you would not expect in public bath. But what is the most important: you can enjoy these activities in intimate environment or in the public space as well. For example: you can take a tea in a bar situated in the sixth floor with exclusive view over opposite hill or you can take different tea in a small informal teahouse hidden in the middle of the disposition. An all-embracing structure of differently juxtaposed reinforced concrete boxes creates a frame for this different human experience.
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Morphological variability of species \kur{Euphrasia stricta} and \kur{Euphrasia nemorosa}
HOŘČICOVÁ, Šárka
Euphrasia L. belongs to the most taxonomically complicated genera in Europe. This is caused especially by considerable similarity of majority of species, intraspecific variation and hybridization, which occurs very often in this genus. A review of the studied genera and hybridization was worked up. Morphological variation of Euphrasia stricta, Euphrasia nemorosa and morphologically intermediate populations was investigated using conventional and geometric morphometric methods. Isolation and optimalization for PCR of ITS, matK and trnT-trnL regions has been made.
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