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Implementing modern species delimitation techniques into fungal taxonomy: Aspergillus charting the course
Sklenář, František ; Hubka, Vít (advisor) ; Haelewaters, Danny (referee) ; Janko, Karel (referee)
This thesis focuses on the implementation of modern methods and approaches for species delimitation in the genus Aspergillus, an economically important fungal genus and model organism. So far, taxonomic studies in Aspergillus regularly included multiple DNA loci (typically four), and the phylogenetic analysis itself mostly consisted of calculating a phylogenetic tree based on individual loci and the concatenated dataset, or less commonly on genealogical concordance principles. Additionally, the datasets usually contained only a limited number of strains per species. The inclusion of more sophisticated phylogenetic species delimitation methods (mostly based on Multispecies coalescent model) in Aspergillus taxonomy adds a whole new layer to the analysis that ensures much higher objectivity of taxonomic decisions. Each of the eight presented papers contains a taxonomic treatment of a particular part of the genus with phylogenetic analyses based on datasets containing DNA sequences from three to six loci or whole genome data (series Nigri). The available molecular data are analyzed by a gradually refined set of phylogenetic species delimitation methods reflecting progress made between years 2017 and 2022. The individual papers also examine some specific characteristics that suitably complement the...
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Taxonomy, diversity and clinical relevance of the genus Aspergillus
Hubka, Vít ; Kolařík, Miroslav (advisor) ; Labuda, Roman (referee) ; de Beer, Wilhelm (referee)
Aspergillus is a speciose genus encompassing nearly 400 species that has significant economic impacts on human health, the food industry, biotechnology and pharmacology. The research included in this thesis focuses on current issues related to the generic concept, subgeneric classification and species delimitation in Aspergillus. It addresses the need for revisions of several sections or species complexes. It provides novel information regarding etiology of aspergillosis as well as the antifungal susceptibilities of several less common opportunistic pathogens. The taxonomic section of the thesis contributes to the taxonomic stability and the new concept of the genus Aspergillus, which changed in response to the discontinuation of dual nomenclature in fungi. Sufficient arguments were collected (e.g., verification of monophyly, unifying phenotypic characters) for maintaining a broad concept of the genus and avoiding splitting it into several genera. All genera typified by sexual morphs and having Aspergillus asexual states were synonymized with Aspergillus and the appropriate names adopted; new combinations were made for teleomorphic species that lacked Aspergillus names. This thesis also contributed to infrageneric taxonomy of the genus via the proposal of four new sections in the subg. Circumdati,...
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Biologická a molekulární charakteristika Cryptosporidium suis-like
VLNATÁ, Gabriela
Cryptosporidium parvum VF383, more commonly known as Cryptosporidium suis-like, has been reported in humans, domesticated ruminants, and wild rats worldwide and described under several names including Cryptosporidium suis-like, based on its close phylogenetic relationship to C. suis. Unlike C. suis, however, it has never been detected in pigs. In the present work, Cryptosporidium suis-like originating from wild brown rats was not infectious for piglets or calves but was infectious for laboratory brown rats, BALB/c mice, and Mongolian gerbils. The prepatent period was 4-5 days for all rodents. The patent period was longer for rats (>30 days) than other rodents (<20 days). None of the rodents developed clinical signs of infection. In all rodents, life cycle stages were detected in the colon by histology and electron microscopy. Oocysts were morphometrically similar to those of C. parvum and smaller than those of C. suis, measuring 5.20 × 4.94 m. Phylogenetic analyses of SSU, actin, and HSP70 gene sequences revealed Cryptosporidium suis-like to be genetically distinct from, C. suis, and other described species of Cryptosporidium. Morphological, genetic, and biological data support the establishment of Cryptosporidium suis-like as a new species, and we propose the name Cryptosporidium occultus sp. n.
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Taxonomy, diversity and clinical relevance of the genus Aspergillus
Hubka, Vít ; Kolařík, Miroslav (advisor) ; Labuda, Roman (referee) ; de Beer, Wilhelm (referee)
Aspergillus is a speciose genus encompassing nearly 400 species that has significant economic impacts on human health, the food industry, biotechnology and pharmacology. The research included in this thesis focuses on current issues related to the generic concept, subgeneric classification and species delimitation in Aspergillus. It addresses the need for revisions of several sections or species complexes. It provides novel information regarding etiology of aspergillosis as well as the antifungal susceptibilities of several less common opportunistic pathogens. The taxonomic section of the thesis contributes to the taxonomic stability and the new concept of the genus Aspergillus, which changed in response to the discontinuation of dual nomenclature in fungi. Sufficient arguments were collected (e.g., verification of monophyly, unifying phenotypic characters) for maintaining a broad concept of the genus and avoiding splitting it into several genera. All genera typified by sexual morphs and having Aspergillus asexual states were synonymized with Aspergillus and the appropriate names adopted; new combinations were made for teleomorphic species that lacked Aspergillus names. This thesis also contributed to infrageneric taxonomy of the genus via the proposal of four new sections in the subg. Circumdati,...
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The global cocoa market
Voglová, Karolína ; Gullová, Soňa (advisor) ; Zamykalová, Miroslava (referee)
This bachelor thesis deals with the global cocoa market. The aim of this thesis is to analyse the global cocoa market and indentify the future prospects of this market. The first chapter deals with the general charakteristics of this commodity, i.e. the history of cocoa growing, types of cocoa, cocoa cultivation and cocoa producing areas, and it is processed by using the methods of synthesis and comparison. Another chapter is the analysis of the global cocoa market, which presents the greatest exporting and importing countries, the developement of cocoa price, cocoa processing and chocolate industry. The third part presents the forms of cocoa trading, i.e. cocoa trading on exchanges and the alternative form fair trade. This part also presents the International Cocoa Organization and International Cococa Initiative. The last chapter focuses on the evaluation and perspectives of the global cocoa market in the future by using the method of compilation. The contribution of this thesis is the determination of the cocoa price and possible solution to the growing demand for cocoa in the future.
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