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Effect of culture medium on the identification of yeasts of the genus Cryptococcus using mass spectrometry
Jurnečková, Alena ; Vadkertiová, Renata (referee) ; Stratilová, Eva (advisor)
Cryptococccus genus is known for its difficult identification and taxonomical classification in area of clinical microbiology. For this bachelor thesis, total 22 yeast strains of the Cryptococcus genus were chosen. The part of strains was firstly analyzed by D1/D2 domain LSU rRNA gene analysis. Three types of culture medium – YPD, potato dextrose agar and Sabouraud’s medium were selected for cultivation. Samples were prepared according to standardized method of Bruker Daltonik company, Institute of Chemistry of SAS and combination of these two methods. Identification was done by MALDI-TOF mass spectrometry. Obtained spectra were compared using corresponding software and evaluated on the basis of specific algorithm. The most advantageous culture medium for cultivation and biotyping with the largest percentage score was YPD (Yeasts pepton dextrose). On the other hand, the least advantageous culture medium was Sabouraud’s agar, which reached the smallest percentage success due to parameters of Bruker Daltonik algorithm. The most succesfull method of sample preparation and application was the combined method with YPD as a culture medium. The results of complete analysis are dendrograms for each medium showing the genetic similarity of yeast strains. The dendrogram shows categorization of the single strains into appropriate groups. Cr. flavescens (CCY 17-3-28, CCY 17-3-30) and Cr. laurentii (CCY 17-3-2) strains were correctly integrated into phylogenetic group Cr. laurentii I (branch in the dendrogram with designation A). Cr. flavus (CCY 17-3-5) doesn’t belong to this group, although it shows similarity with Cr. flavescens. The strains Cr. carnescens (CCY 17-3-13) and Cr. victoriae (CCY 17-3-26) belong to the phylogenetic group Cr. laurentii II (designated as B). Cr. magnus (CCY 17-4-39, CCY 17-4-40) strains show similarity with these strains, but doesn’t belong to the phylogenetic group II. The strains Cr. gastricus (CCY 17-5-1) and Cr. diffluens (non-attached) form a branch designated as C. Cr. aerius (CCY 17-4-9) strain, which was also put into this group, was proposed to sequence analysis, because its spectrum indicates that it should be rather a Cr. diffluens strain. The group D contains Bulleromyces albus (CCY 17-3-35, CCY 17-3-36) and Cr. saitoi (CCY 17-3-18, CCY 17-4-2) strains. The sequenced Cr. albidus (CCY 17-4-1), non-sequenced Cr. diffluens (CCY 17-4-13) and Cr. terreus (CCY 17-8-1) form the group E. The strain CCY 17-4-13 was proposed to sequence analysis because of occurrence of the Cr. diffluens sequenced strain in the group C. The sequenced Cr. aerius (CCY 17-25-1) is also part of this group, but it represents a separate branch. The last group is named as F and consists of Cr. macerans (CCY 17-19-3) and control strains Cr. neoformans var. neoformans (CCY 17-1-4, CCY 17-1-5).
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Biotyping of ascomycetous yeasts
Jurnečková, Alena ; Dudášová,, Hana (referee) ; Stratilová, Eva (advisor)
In total, 84 yeast strains (originated from water, plants, fruits and soil) were selected for MALDI-TOF biotyping. All strains were cultivated on malt agar and YPD medium. Samples for biotyping were processed according to methods of Bruker Daltonik GmbH company, Institute of Chemistry of SAS and combination of these methods. Single strains were identified based on the analysis of intracellular ribozomal proteins using MALDI-TOF mass spectrometry. In case of ambiguous results, the DNA was isolated and the D1/D2 26S rRNA domain sequencing was performed. The strain identification was carried out by comparing its mass spectra with spectra of sequenced strains using MALDI Biotyper 3.0 software. The mutual similarity of strains was considered by score value, which was the result of the analysis. In total, 18 strains from 84 were previously sequenced and used as model strains for comparison with unknown isolates. Altogether 51 strains were definitely taxonomically categorized into 18 phylogenetic groups at the species level. The MALDI-TOF biotyping was repeated for overall 6 strains because of ambiguity of results. The taxonomic classification of 15 strains was not clearly determined and, therefore, these strains were suggested for D1/D2 26S rRNA domain sequencing. It was not possible to identify one strain, based on the results of sequencing, therefore, the DNA isolation was repeated. In the case of 8 strains, the results were identical with originally designed taxonomic classification. Conversely, the remaining 6 strains were identified as species. For 20 selected strains the basic characteristics were determined using microbiological methods. The shape of colonies growing on solid medium and appearance of cultures in liquid medium was assessed. Furthermore, the radial growth constant and the presence of urease were determined. Finally the microscopic observation of cells and the fermentation test for carbohydrate substrates were performed.
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Yeasts of polyphyletic genus Cryptococcus - characteristics and occurence in the nature
Švecová, Natália ; Stratilová,, Eva (referee) ; Schusterová,, Hana (advisor)
Yeasts of genus Cryptococcus belong to the Basidiomycetes, a wide group with different geographical sharing in nature. Many of them rank among human pathogens that endanger immunocompromised patients. Thanks to the big diversity at the level of subspecies, various species of the genus Cryptococcus show different molecular characteristics. Their identification is difficult because of the presence of polysaccharide capsule that surrounds the cell of some species. This work deals with the identification of species occurring in meadows and gardens. The 79 yeasts samples are identified by MALDI-TOF MS. The influence of different culture media on the identification results is monitored simultaneously with the identification. Since a capsule is present in many species, another parameter to be monitored is the influence of the sample preparation method and the matrix on the identification. 51 samples of yeasts of the genus Cryptococcus are identified at the species level in the experimental part. Selected samples are further subjected to the determination of characteristics by conventional microbiological methods. The determined parameters are the presence of urease, radial growth constant, susceptibility to antimycotics, fermentation and assimilation of sugars, growth in the presence of alcohols and growth in the absence of vitamins. The yeast samples are classified into yeast species based on microbiological results. Biotyping resulted in identification of selected samples in the species Filobasidium magnum, Filobasidium oeirense and Filobasidium wieringae. Other samples showed ambiguous identification. As these species have the same properties, they could not be distinguished by the selected microbiological tests.
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Bakteriální kontaminace rybích produktů - mikrobiologický a MALDI TOF přístup
GÁPOVÁ, Pavlína
This diploma thesis was focused on microbial contamination of fish meat. Common carp (Cyprinus carpio) was chosen as a model fish. The work aimed to optimize the conditions for bacterial growth using four different growth media and three different temperatures. Incubation took place at 0, 72 and 120 hours after killing the fish and the samples were incubated at 0, 4 and 8 ° C. Agars selected from a broth of common carp (Cyprinus carpio), grass carp (Ctenopharyngodon idella), rainbow trout (Oncorhynchus mykiss) were used as growth media and a commonly used bovine-based agar was added as a control. After incubation, the obtained bacterial colonies were analyzed by MALDI-TOF MS. At the same time, two chemical analyzes were performed on other meat samples stored under the same conditions. The first was to determine how the content of ATP and its metabolites (Hx + R and Hx) will change over time. The second analysis focused on the change in lactate content over time. The work was divided into 4 phases. The most demanding phase of the whole project, both time and manual, was the preparation of samples for testing and MALDI-TOF MS. The content of ATP and lactate in the meat was detected by high-performance liquid chromatography-ultraviolet (HPLC-UV). The results of the work did not show the influence of the composition of the growth medium on the final microbial community. Temperature proved to be the most significant factor influencing the growth of microorganisms. Bacteria demonstrably grew more and faster at higher temperatures. The lowest and slowest growth was recorded for samples growing at 0 ° C. The second important factor, mainly influencing the species composition of the bacterial community, was the time from the killing of the fish to the time of testing. While the community was grown on the media vaccinated at 0 and 72 hours after slaughter was relatively diverse, the media vaccinated at 120 hours after slaughter have already succeeded in isolating almost exclusively Pseudomonas spp. Analyzes of the content of ATP and lactate have shown that at lower temperatures - respectively the temperature of 0 ° C there is not only a significant slowing down of bacterial growth but also a slowing down of the autolysis process. Differences in storage at 4 and 8 ° C were no longer significantly different.
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Molecular identification of phlebotomine sand flies
Hlavačková, Kristýna ; Dvořák, Vít (advisor) ; Straka, Jakub (referee)
This diploma thesis is focused on species identification of sand flies belonging to two genera of the subfamily Phlebotominae, genus Phlebotomus and Sergentomyia. Genus Phlebotomus together with the genus Lutzomyia of New World include the only proven vectors of Leishmania parasites and they are also carriers of viral and bacterial infections. Species of the genus Sergentomyia are proven vectors of sister genus Sauroleishmania that infects reptiles, but for several decades there have been speculations about their possible involvement in the transmission of mammalian Leishmania species. These suspicions arise mainly from repeated findings of mammalian Leishmania parasites in their digestive system. Correct species determination of medically significant hematophagous arthropods is very important especially for purposes of epidemiological studies so that efficient vector control may be correctly set. Routine identification of sand flies is based on morphological characters located mainly on their heads and genitalia. However, these characters may be variable within a species, they require certain expertise and in the field samples they may be damaged, making proper species identification impossible. This thesis therefore presents two alternatives of sand fly identification based on molecular...
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Analysis of vernix caseosa lipids by chromatografic methods and mass spectrometry
Míková, Radka
(EN) Vernix caseosa is a white creamy substance that covers the skin of a newborn. It is produced during the third trimester by the skin of the baby and remains there until the age of one or even two weeks. It is uniquely human. In utero, vernix protects the skin from maceration, during the birth it serves as a lubricant and after the delivery it protects the baby against infection and regulates the temperature. As vernix is produced in third trimester, prematurely born infants lack it and this may lead to, among other things, suffering from desiccation and therefore heat loss. It is important to study it thoroughly and to find a suitable substitute of vernix for the preterm infants. Vernix consists of lipids, proteins and 80 % water. This project is aimed at the lipids. Vernix is composed of 10 % of lipids. Basic analytical methods of pocessing vernix were searched. The methods of isolation, separation and transesterification have been optimized for the lipids. For separation, thin-layer chromatography has been chosen. The method of the lipid analysis of intact molecules by MALDI-TOF MS has been optimized for these lipids. The results were confirmed using fragmentation spectra and transesterification. Esterified lipids were measured by gas chromatography coupled with mass spectrometry detection....
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Ionic polyacetylene type polymers and polymer networks by catalyst-free quaternization polymerization
Faukner, Tomáš
(Doctoral Thesis, 2016, Mgr. Tomáš Faukner, IONIC POLYACETYLENE TYPE POLYMERS AND POLYMER NETWORKS BY CATALYST FREE QUATERNIZATION POLYMERIZATION) The composition and structure of a series of ionic π-conjugated poly(monosubstituted acetylene)s prepared via catalyst-free quaternization polymerization (QP) of 2-ethynylpyridine (2EP) activated with equimolar amount of alkyl halide [RX = ethyl bromide, ethyl iodide, nonyl bromide and haxadecyl (cetyl) bromide] as a quaternizing agent (QA) have been studied in detail. The performed QPs gave ionic polymers well soluble in polar solvents, with approximately half of pyridine rings quaternized, which implies that also non-quaternized monomers were involved in the process of QP. The configurational structure of polyacetylene main chains was suggested based on 1 H NMR, IR as well as Raman (SERS) spectral methods. The QPs in bulk gave more expected irregular cis/trans polymers while the QPs in acetonitrile solution gave high-cis polymers. A series of prepared symmetrical bi-pyridylacetylene based monomers has been polymerized via QP approach resulting into a series of new ionic π-conjugated poly(disubstituted acetylene) type materials. It is therefore obvious that the mechanism of quaternization activation frequently applied on monosubstituted...
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Yeasts of polyphyletic genus Cryptococcus - characteristics and occurence in the nature
Švecová, Natália ; Stratilová,, Eva (referee) ; Schusterová,, Hana (advisor)
Yeasts of genus Cryptococcus belong to the Basidiomycetes, a wide group with different geographical sharing in nature. Many of them rank among human pathogens that endanger immunocompromised patients. Thanks to the big diversity at the level of subspecies, various species of the genus Cryptococcus show different molecular characteristics. Their identification is difficult because of the presence of polysaccharide capsule that surrounds the cell of some species. This work deals with the identification of species occurring in meadows and gardens. The 79 yeasts samples are identified by MALDI-TOF MS. The influence of different culture media on the identification results is monitored simultaneously with the identification. Since a capsule is present in many species, another parameter to be monitored is the influence of the sample preparation method and the matrix on the identification. 51 samples of yeasts of the genus Cryptococcus are identified at the species level in the experimental part. Selected samples are further subjected to the determination of characteristics by conventional microbiological methods. The determined parameters are the presence of urease, radial growth constant, susceptibility to antimycotics, fermentation and assimilation of sugars, growth in the presence of alcohols and growth in the absence of vitamins. The yeast samples are classified into yeast species based on microbiological results. Biotyping resulted in identification of selected samples in the species Filobasidium magnum, Filobasidium oeirense and Filobasidium wieringae. Other samples showed ambiguous identification. As these species have the same properties, they could not be distinguished by the selected microbiological tests.
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Ionic polyacetylene type polymers and polymer networks by catalyst-free quaternization polymerization
Faukner, Tomáš
(Doctoral Thesis, 2016, Mgr. Tomáš Faukner, IONIC POLYACETYLENE TYPE POLYMERS AND POLYMER NETWORKS BY CATALYST FREE QUATERNIZATION POLYMERIZATION) The composition and structure of a series of ionic π-conjugated poly(monosubstituted acetylene)s prepared via catalyst-free quaternization polymerization (QP) of 2-ethynylpyridine (2EP) activated with equimolar amount of alkyl halide [RX = ethyl bromide, ethyl iodide, nonyl bromide and haxadecyl (cetyl) bromide] as a quaternizing agent (QA) have been studied in detail. The performed QPs gave ionic polymers well soluble in polar solvents, with approximately half of pyridine rings quaternized, which implies that also non-quaternized monomers were involved in the process of QP. The configurational structure of polyacetylene main chains was suggested based on 1 H NMR, IR as well as Raman (SERS) spectral methods. The QPs in bulk gave more expected irregular cis/trans polymers while the QPs in acetonitrile solution gave high-cis polymers. A series of prepared symmetrical bi-pyridylacetylene based monomers has been polymerized via QP approach resulting into a series of new ionic π-conjugated poly(disubstituted acetylene) type materials. It is therefore obvious that the mechanism of quaternization activation frequently applied on monosubstituted...
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Ionic polyacetylene type polymers and polymer networks by catalyst-free quaternization polymerization
Faukner, Tomáš ; Zedník, Jiří (advisor) ; Balcar, Hynek (referee) ; Sedlařík, Vladimír (referee)
(Doctoral Thesis, 2016, Mgr. Tomáš Faukner, IONIC POLYACETYLENE TYPE POLYMERS AND POLYMER NETWORKS BY CATALYST FREE QUATERNIZATION POLYMERIZATION) The composition and structure of a series of ionic π-conjugated poly(monosubstituted acetylene)s prepared via catalyst-free quaternization polymerization (QP) of 2-ethynylpyridine (2EP) activated with equimolar amount of alkyl halide [RX = ethyl bromide, ethyl iodide, nonyl bromide and haxadecyl (cetyl) bromide] as a quaternizing agent (QA) have been studied in detail. The performed QPs gave ionic polymers well soluble in polar solvents, with approximately half of pyridine rings quaternized, which implies that also non-quaternized monomers were involved in the process of QP. The configurational structure of polyacetylene main chains was suggested based on 1 H NMR, IR as well as Raman (SERS) spectral methods. The QPs in bulk gave more expected irregular cis/trans polymers while the QPs in acetonitrile solution gave high-cis polymers. A series of prepared symmetrical bi-pyridylacetylene based monomers has been polymerized via QP approach resulting into a series of new ionic π-conjugated poly(disubstituted acetylene) type materials. It is therefore obvious that the mechanism of quaternization activation frequently applied on monosubstituted...
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