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Monitoring of the influence of using indigenous yeasts for wine production in the conditions of winery
Beníčková, Romana ; Vadkertiová, Renata (referee) ; Vránová, Dana (advisor)
This thesis deals with identification of yeasts by applying the RFLP-PCR method. Objective of the thesis was to identify the yeasts present in wine from Grüner Veltliner during fermentation. Identification was made by amplification of 5,8S-ITS sequences of DNA by the polymerase chain reaction with primers ITS1 and ITS4. Amplified DNA was submitted to the restriction analysis by restriction endonuclease HaeIII, HinfI and HhaI. By restriction analysis with a specific enzyme, the amplified DNA is chopped into the specific fragments which are characteristic for given kind of yeasts. In the analysed wine, the dominance of autochthonal yeast Saccharomyces cerevisiae was confirmed throughout fermentation. The other identified yeasts in the wine were of kind Pichia. The second part of the thesis was to expand the database by characterization of 28 type-yeasts, using RFLP-PCR analysis. To compare the genetic similarity, program BioNumerics was used, which processed the results of UPGMA cluster analysis using Jaccard´s coefficients.
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Tool for Classification of Lifestyle Traits Based on Metagenomic Data from the Large Intestine
Kubica, Jan ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
This thesis deals with analysis of human microbiome using metagenomic data from large intestine. The main focus is placed on bacteria composition in a sample on different taxonomic levels regarding the lifestyle traits of an individual. For this purpose, a tool for classification of several attributes was created. It considers attributes like diet type and eating habits (vegetarian, vegan, omnivore), gluten and lactose intolerance, body mass index, age or sex. From range of machine learning perspectives considering K Nearest Neighbours (kNN), Random Forest (RF) and Support Vector Machines (SVM) were used. Datasets for training and final evaluation of the classifier were taken from American Gut project. The thesis also focuses on particular problems with metagenomic datasets like its multidimensionality, sparsity, compositional character and class imbalance.
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Bacteria Classification Based on Marker Genes
Pelantová, Lucie ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
The aim of this work is proposal of new method for bacteria classification based on sequences of marker genes. For this purpose was chosen 10 marker genes. Resulting MultiGene classifier processes data set by dividing it in several groups and choosing gene for each group which can distinguish this group with best results. This work describes implementation of MultiGene classifier and its results in comparison with other bacteria classifiers and with classification based entirely on gene 16S rRNA.
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Evaluation of Organisms Relationship by Genomic Signal Processing
Škutková, Helena ; Tkacz, Ewaryst (referee) ; Schwarz,, Daniel (referee) ; Provazník, Ivo (advisor)
This dissertation deals with alternative techniques for analysis of genetic information of organisms. The theoretical part presents two different approaches for evaluation of relationship between organisms based on mutual similarity of genetic information contained in their DNA sequences. The first approach is currently standardized phylogenetics analysis of character based records of DNA sequences. Although this approach is computationally expensive due to the need of multiple sequence alignment, it allows evaluation of global and local similarity of DNA sequences. The second approach is represented by techniques for classification of DNA sequences in a form of numerical vectors representing characteristic features of their genetic information. These methods known as „alignment free“ allow fast evaluation of global similarity but cannot evaluate local changes. The new method presented in this dissertation combines the advantages of both approaches. It utilizes numerical representation similar to 1D digital signal, i.e. representation that contains specific trend along x-axis. The experimental part of dissertation deals with design of a set of appropriate tools for genomic signal processing to allow evaluation mutual similarity of taxonomically specific trends. On the basis of the mutual similarity of genomic signals, the classification in the form of dendrogram is applied. It corresponds to phylogenetic trees used in standard phylogenetics.
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Taxonomy of yeasts of the genus Saccharomyces
Augustová, Kamila ; Vadkertiová, Renata (referee) ; Vránová, Dana (advisor)
The theoretical part discusses the yeasts and their taxonomic classification using traditional methods and using modern methods. Detail the work is concerned with descriptions of modern molecular-biology methods. The practical part was analyzed DNA by PCR-fingerprinting (rep-PCR) type of yeasts, which we received from the CCY and subsequent analysis of yeast samples obtained from grape musts. One of the grape must was obtained in 2009 (white grape variety) and the second in 2010 (red grape variety). Both grape musts come as integrated vineyards and organic. Grape musts samples were obtained from the winery Holánek from Ivaň. The cross-comparison of images PCR-fingerprint type yeasts and yeasts PCR-fingerprint samples using BioNumerics was to evaluate the results and conclude that the diversity of yeast flora in grape must.
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One Health approach to understand emerging zoonotic pathogens in the Trichophyton benhamiae complex
Čmoková, Adéla ; Hubka, Vít (advisor) ; Buchta, Vladimír (referee) ; Gené, Josepa (referee)
The Trichophyton benhamiae complex encompasses several zoonotic pathogens that are of increasing concern to the scientific community due to their epidemic spread among pets and their owners. Of particular concern is the sudden appearance and rapid spread of T. benhamiae yellow phenotype strains in Europe. Considerable genetic and phenotypic variability has been revealed in the pathogens from the complex, yet the species limits and host spectra have not been clearly elucidated. To explore the diversity, epidemiology, and taxonomy of the T. benhamiae complex, my colleagues and I formed an international, cross-disciplinary team and applied a holistic One Health approach. We collected a large dataset of strains from several continents, along with associated data about host, clinical picture, and locality. Due to the high level of clonality in commonly used DNA sequence markers, I developed a new typing schema based on ten microsatellite markers and four DNA sequence markers. We then used a polyphasic approach combining data from independent analyses to decide on species limits in the T. benhamiae complex, including phylogenetic and population-genetic analyses, phenotypic and physiological analyses, mating-type gene characterization, ecological data and MALDI- TOF mass spectrometry analysis. Thanks to...
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Taxonomy, phylogeny and phylogeografy of selected groups of aquatic beetles (Coleoptera: Hydrophilidae, Hydraenidae) of the Caribbean region
Deler-Hernández, Albert ; Fikáček, Martin (advisor) ; Ribera, Ignacio (referee) ; Archangelsky, Miguel (referee)
This thesis is focused in the representatives of beetle families Hydrophilidae and Hydraenidae of West Indies and adjacent regions. It consists of two parts, the phylogenetic part and the systematic part. The phylogenetic part focuses on the hydrophilid genera Phaenonotum and Crenitulus of Greater Antilles: beetles were sampled in all four main islands (Cuba, Hispaniola, Puerto Rico and Jamaica) and analyzed using the combination of molecular and morphological data. The genus Phaenonotum contains four single-island endemics, of which those from Cuba, Jamaica and Hispaniola are wingless and form a clade that diversified ca. 46 million years ago (Ma) and likely colonized the Caribbean via the GAARlandia land bridge. In contrast, the Puerto Rican endemic and the two remaining non-endemic species colonized the Greater Antilles by over- water dispersal during the Oligocene-Miocene. The analysis of the genus Crenitulus revealed that Greater Antillean species belong to two separate clades: the Crenitulus yunque clade endemic for Cuba and Hispaniola, and the Crenitulus suturalis clade containing specimens from Greater Antilles and from northern America. A detailed revision of the Crenitulus yunque clade using morphology and molecular-based species delimitation recognized 11 species locally endemic for...
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Diversity, ecology, and biotechnological potential of yeasts associated with bark beetles
Havlíček, Václav ; Kolařík, Miroslav (advisor) ; Novotný, David (referee)
Bark beetles (Coleoptera; Scolytinae) attack woody plants, which is why they are considered pests from a human perspective. They owe their evolutionary success, among other factors, to numerous symbioses with microorganisms, with fungi playing a significant role. The mycobiome of bark beetles is dominated by yeasts, which, nevertheless, are widely overlooked. Intestinal yeasts not only from Ips typographus but also from other species of bark beetles have potential for future biotechnological applications. The aim of this study was to examine their diversity and physiological activities, which will help clarify their ecological role and biotechnological potential. Collections were conducted in the Czech Republic from larvae of the spruce bark beetle Ips typographus and from various species of subcortical insects in Kenya. Yeasts were identified and taxonomically classified based on rDNA sequencing. A total of 133 yeast strains belonging to 37 species were identified, including 9 species that could not be identified and belong to previously undescribed species and in two cases also genera. A total of 133 yeast strains belonging to 37 species were identified, including 9 species that could not be identified and belong to previously undescribed species and in two cases also genera. The most frequently...
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Taxonomic overview of the genus Arthroderma with focus on species associated with reptiles and bats
Kolarczyková, Daniela ; Hubka, Vít (advisor) ; Dobiáš, Radim (referee)
The genus Arthroderma belongs to a group of geophilic dermatophytes that primarily degrade keratin in soil and occasionally cause infections in humans and animals. This species-rich genus has received particular attention in recent years in terms of species occurring in human clinical material or clinical samples isolated from rodents and other mammals, which has been associated with a significant increase in the number of its species. In this thesis, the species diversity of the genus Arthroderma was investigated in material isolated from snakes, bats and cave sediment, a substrate that has been almost unexplored in terms of the occurrence of this genus. The strains studied were isolated during research on bats diseased by "white nose syndrome" and snakes by "snake fungal disease". In the past, the genus Arthroderma has been studied either on the basis of morphology or, after the advent of molecular methods, in terms of multigene phylogeny. However, no monographs have simultaneously combined phenotypic and molecular genetic criteria to assess species boundaries across the genus or a significant part of it. This is one of the reasons why species boundaries are often unclearly defined. Thus, another aim of this work was to improve the multigene phylogeny of the genus by incorporating new strains,...
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Morphological and ecological differentiation and distribution of taxa in the Galium mollugo group
Talpová, Julie ; Kaplan, Zdeněk (advisor) ; Štech, Milan (referee)
My thesis deals with three taxa of the polyploid complex Galium mollugo that occur in the Czech Republic. These are diploid G. mollugo and tetraploid G. album subsp. album and G. album subsp. pycnotrichum. These taxa are very similar to each other, their identification is difficult and exact values of the quantitative characters used for their separation are unknown. To date, there has been no study based on flow cytometry (FCM) and classical morphometrics analysis in this complex. By using them I wanted to bring new results and fill the gaps in scientific research. Primarily, I was investigating whether the individual cytotypes can be distinguished based on different genome size using FCM analyses. Another aim was to determine whether it is possible to define morphological and ecological differences between diploid and tetraploid taxa. The morphometrics included ordination and discrimination methods. I observed whether taxa could be distinguished by the naked eye and determined by measurement which characters are most suitable for identification. FCM analyses proved to be suitable to distinguish the two ploidy levels. I have been able to demonstrate by statistical methods that diploid and tetraploid taxa differ from each other, and I have also refined the characters that are most suitable for...
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