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Tracing Microendolithic Ichnocenoses: A paleoecological and taphonomic approach over the Phanerozoic
Herenio Kerkhoff, Marta Leticia ; Holcová, Katarína (advisor) ; Skupien, Petr (referee) ; Soták, Ján (referee)
The microbial endoliths study from the Western Carpathians region was a semi-quantitative survey that included six sampling localities. Samples, ranging from Upper Oligocene to Miocene (Serravalian), came from three localities in Czechia (Mikulov, LOM-1 and Hevlín), two in Slovakia (DNV and LKŠ) and one place in Hungary (Tard Clays, Rozalia Quarry). The main goal of this project was to verify how different levels of hypoxia, established for studied intervals, would affect the microendolilthic assemblages present in tests of benthic foraminifera. Additionally, microbial activity and byproducts, and the overall interplay between bioerosion and bioprecipitation are also analysed. The degree of hypoxy was established using ratio of oxic/dysoxic and hypoxic foraminifera, defined as Benthic Foraminifera Oxygen Index (BFOi) Sampled index shows a predominance of dysoxic indicators, with rare oxic elements. Secondary electron elemental analysis (EDX) reveals a significant enrichment of sulphur, phosphorus and iron in biofilm samples from DNV and Hevlín, when compared to the rock matrix surrounding it. Resin casts reveal a predominance of Dysphotic to Deep Euphotic zones ichnocenosis, with a predominance of Chlorophyte, Rodophyte and heterotroph burrows. Few representatives of Cyanobacteria traces, such as...
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Contributions to the taxonomy, biogeography, ecology and pathogens of parasites (Diptera, Acari) of Old World bats
Ševčík, Martin ; Benda, Petr (advisor) ; Stanko, Michal (referee) ; Bartonička, Tomáš (referee)
The dissertation thesis presents contributions solving several faunistic, biogeographical, taxonomic, and phylogenetic problems of selected groups of bat parasites together with surveys of potential pathogens in some representatives of these parasitic groups linked to the bats of the Old World. In the first part of the thesis, the taxonomy of prostigmata mites - chiggers (Trombiculidae) - coming from Eurasia and Africa is elaborated. Results of a detailed morphological and morphometric study are the descriptions of five new taxa belonging to four genera: Chiroptella, Grandjeana, Rudnicula, and Trombicula. At the same time, the results revise the differentiation within the group Trombicula sensu stricto, summarize the findings of species of individual genera and correct the inclusions of the originally described species within individual genera, with the final output of creating identification keys to the genera. The first sketch of the results of the study of the relations between chiggers and bats is included in this section, representing the description of the specific links among individual segments of both groups. In addition, there are studies presenting new findings and morphometric examinations of velvet mite nymphs collected from bats in Indonesia, as well as morphometric data and...
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Phylogeographic and systematic studies of selected bat taxa of the western part of the Old World
Uvizl, Marek ; Benda, Petr (advisor) ; Bryja, Josef (referee) ; Csorba, Gabor (referee)
Bats attract attention due their extraordinary adaptations including their ability to actively fly and echolocate, and extended lifespan, phenotypic diversity, etc. The phylogeny was analysed using cutting-edge molecular methods. However, the molecular revision of several species and species groups is still pending, especially those with wide distribution ranges or cryptic species complexes, even in the western part of the Old World. This specification encompasses Europe, the Middle East, Central Asia, and Africa and it represents the traditional research area for Central European (Czech and Czechoslovak) bat researchers. In my PhD thesis, I aimed to revise the phylogenetic and phylogeographic relationships of six less studied species and/or species groups of bats, using a combination of molecular and morphological phylogenetic approaches. The sequences of both mitochondrial and nuclear genetic markers were generated from over 10 species. These sequences were used to construct phylogenetic trees, haplotype networks, and estimate the time of divergence of studied species. The main results of my PhD thesis were: (1) filling gaps in the knowledge of the distribution ranges of species from the M. nattereri species complex (Vespertilionidae) by including and identifying samples from the Middle East; (2)...
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Yeasts and wine
Palíková, Petra ; Vadkertiová, Renata (referee) ; Vránová, Dana (advisor)
This thesis deals with isolation and identification wine yeasts from grapes and must. For analysis was used white wine Sauvignon that was grown and producing after needs ecological agriculture. Remove samples were processed in laboratory and by the help of dilution method were obtained pure culture isolated yeasts. In the following step, by the application of commercial kit UltraCleanTM Microbial DNA Isolation Kit we were able to isolated individual DNA that it was used to the next analysis. Isolated DNA was amplification by PCR method with ITS1 and ITS4 primers. PCR products were detected on agarose gel. Amplification samples were chopped five restriction endonucleases: HaeIII, HinfI, TaqaI, AluI and MseI. Chopped DNA was detected by the same way as PCR products and it was compared with restriction patterns of collection yeasts. In the next step it was compared genetic similarity of isolated yeasts by using BioNumerics software. As a criterion it was used Pearson coefficients and UPGMA clastering analysis. The result is dedrogram of genetics similarity isolated yeasts.
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Bioinformatic Tool for Classification of Bacteria into Taxonomic Categories Based on the Sequence of 16S rRNA Gene
Valešová, Nikola ; Hon, Jiří (referee) ; Smatana, Stanislav (advisor)
Tato práce se zabývá problematikou automatizované klasifikace a rozpoznávání bakterií po získání jejich DNA procesem sekvenování. V rámci této práce je navržena a popsána nová metoda klasifikace založená na základě segmentu 16S rRNA. Představený princip je vytvořen podle stromové struktury taxonomických kategorií a používá známé algoritmy strojového učení pro klasifikaci bakterií do jedné ze tříd na nižší taxonomické úrovni. Součástí práce je dále implementace popsaného algoritmu a vyhodnocení jeho přesnosti predikce. Přesnost klasifikace různých typů klasifikátorů a jejich nastavení je prozkoumána a je určeno nastavení, které dosahuje nejlepších výsledků. Přesnost implementovaného algoritmu je také porovnána s několika existujícími metodami. Během validace dosáhla implementovaná aplikace KTC více než 45% přesnosti při predikci rodu na datových sadách BLAST 16S i BLAST V4. Na závěr je zmíněno i několik možností vylepšení a rozšíření stávající implementace algoritmu.
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Virtual Herbarium with e-Learning Features
Semmler, Jiří ; Burget, Radek (referee) ; Rychlý, Marek (advisor)
This thesis is concerned with analysis, design and implementation web information system for management of virtual digital herbarium for high or middle schools. Online available services can not provide any alternative where students can cooperate with teachers in creating own virtual digital herbarium. This service provides a platform for creating own collection of pictures of plants with stress on their categorization to the taxonomy, detailed description, checking plagiarism and communication between students and teachers.
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Optimalization of PCR-RFLP method for taxonomy of yeasts
Olivová, Radana ; Vadkertiová, Renata (referee) ; Vránová, Dana (advisor)
This thesis deal with optimalization method PCR – RFLP for taxonomy enlistment of yeasts. Conventional identification methods for yeasts are time-consuming. Molecular biological method based on PCR are instrumental towards fast and precise identification as compared to conventional phenotypic methods. In this thesis molecular biological method PCR – RFLP was used for identification and enlistment of yeasts. This metod follow repeating spacers of ribozomal DNA of yeast, characteristic for each species and strain. By the help of PCR were amplified specific partitions of DNA. These fragments of DNA were split by restriction endonucleases and identified by horizontal electroforesis. In background of this thesis there are information about yeasts, their taxonomy and molecular biological methods.
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Code Characterization for Automated User Interface Generation
Kadlec, Jaroslav ; Slavík,, Pavel (referee) ; Sochor, Jiří (referee) ; Zemčík, Pavel (advisor)
Práce představuje nový přístup v automatizovaném vytváření uživatelských rozhraní. Na základě taxonomie pro charakterizaci dat byla vyvinuta nová taxonomie pro charakterizaci kódu. Tato taxonomie označuje významné vlastnosti dat a kódu tak, aby ji bylo možné použít v procesu automatického vytvoření uživatelského rozhraní. Taxonomie je platformově nezávislá a může být uložena jako součást metadat nebo v externím souboru. Na základě taxonomie je představený proces automatického vytvoření uživatelského rozhraní s detailnějším popisem jednotlivých kroků. Celý proces generování uživatelského rozhraní je demonstrován na příkladech.
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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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