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Biodiversity of Myxozoa based on extensive screening of fish and environmental samples
LISNEROVÁ, Martina
2022 - English
Myxozoans represent a group of morphologically simplified endoparasites infecting mainly fish, annelid and bryozoan hosts including more than 2,600 nominal species. However, the diversity seems to be unexplored and undervalued. Host searching and invasive dissection is a commonly used method for the identification of myxozoan species diversity. Metabarcoding and amplicon analyses of environmental DNA from sediment, water and soil is developing approach for biodiversity assessment and have been performed in many biological areas to identify the diversity of organisms, communities and populations. Using classical morphological and molecular approaches, we explored the myxozoan diversity in selected areas and host groups. In addition, we propose a new methodological approach for the studying of myxozoan diversity based on environmental DNA from sediment and amplicon sequencing. Illumina Mi-Seq with metabarcoding and newly designed primer sets is suitable for analyzing myxozoan communities without the need to find and capture intermediate or final hosts.
Keywords:
Myxozoa; Diversity; Phylogeny; eDNA; elasmobranchs
Available in the Digital Repository of University of South Bohemia.
Biodiversity of Myxozoa based on extensive screening of fish and environmental samples
Myxozoans represent a group of morphologically simplified endoparasites infecting mainly fish, annelid and bryozoan hosts including more than 2,600 nominal species. However, the diversity seems to be ...
Assembly and analysis of repeat-rich regions of plant genomes
VONDRAK, Tihana
2022 - English
Satellite DNA has been identified in varying proportions in many eukaryotic genomes. It consists of monomeric units arranged in tandem into long, homogeneous arrays. Due to its repetitive nature, satellite DNA is difficult to assemble and analyze, and has therefore been largely neglected in research. With the development of next generation sequencing technologies such as Illumina, research on satellite DNA has intensified and our understanding of it has improved. However, the information we obtain with Illumina reads is limited by their short length. While we can characterize the sequence of satellite DNA and its abundance in genomes, it is not possible to study the long-range organization of satellite DNA, which limits our understanding of the origin and evolution of satellite DNA. This limitation can be addressed by using the latest generation of sequencing technologies that generate much longer reads of tens to hundreds of kilobases. The goal of this work was to develop bioinformatics approaches for analyzing the properties of satellite DNA arrays from long sequence reads or from genome assemblies generated with these reads. These were then used to analyze populations of satellite repeats throughout the genome or in the specific type of chromatin in three plant species that differ in the organization of their centromeres.
Available in the Digital Repository of University of South Bohemia.
Assembly and analysis of repeat-rich regions of plant genomes
Satellite DNA has been identified in varying proportions in many eukaryotic genomes. It consists of monomeric units arranged in tandem into long, homogeneous arrays. Due to its repetitive nature, ...
Interaction of tick-borne encephalitis virus with host and vector cells
TYKALOVÁ, Hana
2022 - English
The proposed thesis deals with the various aspects of tick-borne encephalitis virus infection in the host and the vector on the cellular level. It uncovers transcriptomic and proteomic responses in infected cells in the human neurons and astrocytes, and vector cells. It identifies the subgenomic flaviviral RNA as an important pathogenesis effector that can interfere with the vector RNAi pathway, and at the same time denotes the components of this pathway. It also describes the phenomenon of impairment of host protein and rRNA synthesis upon TBEV infection. Moreover, it uncovers the importance of quasispecies in the adaptation to vector and host cells. The proposed thesis deals with the various aspects of tick-borne encephalitis virus infection in the host and the vector on the cellular level. It uncovers transcriptomic and proteomic responses in infected cells in the human neurons and astrocytes, and vector cells. It identifies the subgenomic flaviviral RNA as an important pathogenesis effector that can interfere with the vector RNAi pathway, and at the same time denotes the components of this pathway. It also describes the phenomenon of impairment of host protein and rRNA synthesis upon TBEV infection. Moreover, it uncovers the importance of quasispecies in the adaptation to vector and host cells.
Keywords:
tick-borne encephalitis virus; tick cells; neural cells; immune response; RNAi pathway; translational shut-off; transcriptional shut-off; quasispecies; transcriptomic; proteomics
Available in the Digital Repository of University of South Bohemia.
Interaction of tick-borne encephalitis virus with host and vector cells
The proposed thesis deals with the various aspects of tick-borne encephalitis virus infection in the host and the vector on the cellular level. It uncovers transcriptomic and proteomic responses in ...
Interactions between plants, herbivorous insect and predators: mechanisms and ecological importance
MRÁZOVÁ, Anna
2022 - English
Práce popisuje interakce mezi třemi trofickými úrovněmi z různých pohledů. Zaměřuje se na roli rostlin, býložravého hmyzu a bezobratlých predátorů a ptáků v trofických interakcích. Konkrétně popisuje nepřímo vyvolanou obranu rostlin a komunikaci rostlin s vyššími taxony a změny v predačním tlaku a společenstvech hmyzu vyvolané obrannými chemickými látkami uvolňovaných z rostlin poškozených herbivory. The thesis describes the interactions between the three trophic levels from different perspectives. It focuses on the role of plants, herbivorous insect, and invertebrate predators and birds in trophic interactions. More specifically, it describes indirectly induced plant defence and communication with higher taxa and changes in predation pressure and insect communities in response to defensive chemical compounds released from herbivory-damaged plants.
Keywords:
Tritrofické interakce; obrana rostlin; býložravý hmyz; predace; ptáci; methyl jasmonát
Available in the Digital Repository of University of South Bohemia.
Interactions between plants, herbivorous insect and predators: mechanisms and ecological importance
Práce popisuje interakce mezi třemi trofickými úrovněmi z různých pohledů. Zaměřuje se na roli rostlin, býložravého hmyzu a bezobratlých predátorů a ptáků v trofických interakcích. Konkrétně popisuje ...
Beneficial and toxic effects of REE in algae and plants
ASHRAF, Nermeen
2022 - English
Lanthanides mainly represented by REE are the most frequently occurring elements as compared to arsenic and lead. REE consist of a group of elements associated with each other in terms of common physical and chemical properties, with studies concerning phytoremediation and physiological effects of such elements on living biota, is important to be addressed as these elements are frequently being considered as emerging pollutants because of excessive mining and release into the environment. Very important is to study the toxic effects of lanthanum in microalgae under environmental conditions. Experimental trials are evaluating especially potential risks on growth and photosynthesis under nanomolar-dose, with promising decrease and acute toxicity. To this end, the two most promising La-binding protein is currently investigated in green microalgae (Desmodesmus quadricauda) with high affinities. Subcellular localization patterns of La have been also shown to predict possible expression sites and to understand the metabolic response of La in microalgae. We also identify accumulator plant species for LREE in contaminated mining areas for phytoremediation purposes, aim of this study was conducted in the Brazilian mining area for REE and as well as identifying the bioavailable content which can help in predicting the promising species. This field study was done for finding new accumulators which are involved in concentrating LREE in above-ground parts. Our study suggests toxic effects of La and identified preferentially good hyperaccumulator plant specie Christella dentata for phytomining of lanthanides. This could be used as a predictive bioaccumulator in phytoremediation and its further analysis can be a part of future studies for insight mechanisms using analytical techniques, involving the identification of La-binding proteins in Desmodesmus quadricauda. Lanthanides mainly represented by REE are the most frequently occurring elements as compared to arsenic and lead. REE consist of a group of elements associated with each other in terms of common physical and chemical properties, with studies concerning phytoremediation and physiological effects of such elements on living biota, is important to be addressed as these elements are frequently being considered as emerging pollutants because of excessive mining and release into the environment. Very important is to study the toxic effects of lanthanum in microalgae under environmental conditions. Experimental trials are evaluating especially potential risks on growth and photosynthesis under nanomolar-dose, with promising decrease and acute toxicity. To this end, the two most promising La-binding protein is currently investigated in green microalgae (Desmodesmus quadricauda) with high affinities. Subcellular localization patterns of La have been also shown to predict possible expression sites and to understand the metabolic response of La in microalgae. We also identify accumulator plant species for LREE in contaminated mining areas for phytoremediation purposes, aim of this study was conducted in the Brazilian mining area for REE and as well as identifying the bioavailable content which can help in predicting the promising species. This field study was done for finding new accumulators which are involved in concentrating LREE in above-ground parts. Our study suggests toxic effects of La and identified preferentially good hyperaccumulator plant specie Christella dentata for phytomining of lanthanides. This could be used as a predictive bioaccumulator in phytoremediation and its further analysis can be a part of future studies for insight mechanisms using analytical techniques, involving the identification of La-binding proteins in Desmodesmus quadricauda.
Keywords:
lanthanides; microalgae; growth; photosynthesis; La-binding protein; subcellular localization; phytoremediation; LREE; hyperaccumulator; Christella dentata
Available in the Digital Repository of University of South Bohemia.
Beneficial and toxic effects of REE in algae and plants
Lanthanides mainly represented by REE are the most frequently occurring elements as compared to arsenic and lead. REE consist of a group of elements associated with each other in terms of common ...
Evolution and Phylogeny of Mesozoa
DRÁBKOVÁ, Marie
2022 - English
This thesis focuses on the phylogenetic position of Mesozoa (Orthonectida and Dicyemida) based on phylogenomics, and on dicyemid life-history traits revealed by molecular methods used in population genetics. The thesis is introduced by the review of biology of both groups, complemented by up to now development of views on their phylogenetic position and notes concerning the study of the population structure of marine invertebrates. The introduction is followed by a study focusing on the phylogenetic position of Mesozoa, a comparison of population structure between the cephalopod host and its dicyemid parasite, and a case study of dicyemid parasite infrapopulation. The thesis wraps up with a review on cephalopod parasites and a summary.
Keywords:
Mesozoa; Dicyemida; Orthonectida; Phylogenomics; Population genetics; Marine biology; Parasites
Available in the Digital Repository of University of South Bohemia.
Evolution and Phylogeny of Mesozoa
This thesis focuses on the phylogenetic position of Mesozoa (Orthonectida and Dicyemida) based on phylogenomics, and on dicyemid life-history traits revealed by molecular methods used in population ...
Effect of distinct soil horizon and vegetation on soil microbiome abundance, composition, and activity of Arctic permafrost
VARSADIYA, Milankumar
2022 - English
In the present work, I studied the abundance, composition, and activity of soil microbial communities involved in the decomposition of soil organic matter (OM) in different horizons and under distinct tundra vegetation of Arctic permafrost soils. Special emphasis was given to buried topsoil caused by cryoturbation processes. The enzyme activity and their stoichiometry were also analyzed to determine the limitation of microbial carbon, nitrogen, and phosphorus. I also applied the metatranscriptomics approach to study the active microbial community in a complex view of all three domains of life (bacteria, archaea, Eukaryota). With this approach, we could better understand the potential role of microbial interactions (e.g., bacterial predation) in the carbon and nitrogen cycles of permafrost soils.
Keywords:
Microbes; Soil organic matter; Climate change; Arctic Permafrost; Tundra Vegetation
Available in the Digital Repository of University of South Bohemia.
Effect of distinct soil horizon and vegetation on soil microbiome abundance, composition, and activity of Arctic permafrost
In the present work, I studied the abundance, composition, and activity of soil microbial communities involved in the decomposition of soil organic matter (OM) in different horizons and under distinct ...
Study of Cancer Immunotherapy Mechanisms in Pancreatic Adenocarcinoma and Pheochromocytoma Murine Models
UHER, Ondřej
2022 - English
This dissertation examines the study of intratumoral cancer immunotherapy using a combination of phagocytosis-stimulating ligands and Toll-like receptor ligands (TLR) in murine pancreatic adenocarcinoma and pheochromocytoma murine models. In this study, we show that intratumoral application of the phagocytosis-stimulating ligand Mannan-BAM and three TLR ligands, referred to as MBT therapy, efficiently suppresses tumor growth in more than 83% of mice bearing murine melanoma. However, in aggressive pancreatic adenocarcinoma and pheochromocytoma murine models, such a combination is inefficient and must be combined with an agonistic anti-CD40 antibody, referred to as MBTA therapy, to achieve complete eradication of the tumor. We show that complex intratumoral MBTA therapy can systemically increase the recruitment of innate immune cells followed by activation of adaptive immune cells not only in treated tumors but also in distal non-treated lesions, resulting in the reduction of tumor growth and prolonged survival of treated mice. Taken together, these findings highlight the effect of MBTA therapy and the potential to optimize this therapeutic approach for future use in clinical trials as a treatment for metastatic cancers. This dissertation examines the study of intratumoral cancer immunotherapy using a combination of phagocytosis-stimulating ligands and Toll-like receptor ligands (TLR) in murine pancreatic adenocarcinoma and pheochromocytoma murine models. In this study, we show that intratumoral application of the phagocytosis-stimulating ligand Mannan-BAM and three TLR ligands, referred to as MBT therapy, efficiently suppresses tumor growth in more than 83% of mice bearing murine melanoma. However, in aggressive pancreatic adenocarcinoma and pheochromocytoma murine models, such a combination is inefficient and must be combined with an agonistic anti-CD40 antibody, referred to as MBTA therapy, to achieve complete eradication of the tumor. We show that complex intratumoral MBTA therapy can systemically increase the recruitment of innate immune cells followed by activation of adaptive immune cells not only in treated tumors but also in distal non-treated lesions, resulting in the reduction of tumor growth and prolonged survival of treated mice. Taken together, these findings highlight the effect of MBTA therapy and the potential to optimize this therapeutic approach for future use in clinical trials as a treatment for metastatic cancers.
Keywords:
intratumoral; immunotherapy; cancer; pancreatic adenocarcinoma; pheochromocytoma
Available in the Digital Repository of University of South Bohemia.
Study of Cancer Immunotherapy Mechanisms in Pancreatic Adenocarcinoma and Pheochromocytoma Murine Models
This dissertation examines the study of intratumoral cancer immunotherapy using a combination of phagocytosis-stimulating ligands and Toll-like receptor ligands (TLR) in murine pancreatic ...
The relationships among functional traits of tardigrades (Tardigrada), their diet, and environmental conditions
TŮMOVÁ, Michala
2022 - English
In this thesis, I explore several ways how to use functional traits to study the tardigrade role in the soil food web. The goal of the thesis was to show that it is possible to study tardigrade ecology even without species identification. Trophic classification of tardigrades, as well as morphometric traits of each individual, were used as functional traits. First, I confirmed the existence of different trophic groups, testing the whole spectrum of potential diet in three tardigrade species from different trophic groups. I showed that tardigrades differed not only in the scope of ingested items but also in survival and fecundity under different types of diet. Secondly, I compared trophic group composition with species composition in natural tardigrade communities. The results showed that species, as well as trophic group composition, responded to the same environmental drivers. Trophic group composition enabled easier interpretation of the tardigrade role in the soil food web, while species composition illustrated also species-specific preferences that were not connected to their feeding habits such as preferences for different levels of soil moisture. Finally, I have used morphometric traits measured in each individual separately which allowed me for evaluation of inter-specific as well as intra-specific variation. As a result, buccal tube length was selected as a predictor of tardigrade feeding preferences among nematode, rotifer, and tardigrade prey. In summary, the thesis documented that functional traits provide a tool for the prediction of tardigrade feeding behaviour and detection of changes in the role of tardigrades along environmental gradients without the need of species identification. In this thesis, I explore several ways how to use functional traits to study the tardigrade role in the soil food web. The goal of the thesis was to show that it is possible to study tardigrade ecology even without species identification. Trophic classification of tardigrades, as well as morphometric traits of each individual, were used as functional traits. First, I confirmed the existence of different trophic groups, testing the whole spectrum of potential diet in three tardigrade species from different trophic groups. I showed that tardigrades differed not only in the scope of ingested items but also in survival and fecundity under different types of diet. Secondly, I compared trophic group composition with species composition in natural tardigrade communities. The results showed that species, as well as trophic group composition, responded to the same environmental drivers. Trophic group composition enabled easier interpretation of the tardigrade role in the soil food web, while species composition illustrated also species-specific preferences that were not connected to their feeding habits such as preferences for different levels of soil moisture. Finally, I have used morphometric traits measured in each individual separately which allowed me for evaluation of inter-specific as well as intra-specific variation. As a result, buccal tube length was selected as a predictor of tardigrade feeding preferences among nematode, rotifer, and tardigrade prey. In summary, the thesis documented that functional traits provide a tool for the prediction of tardigrade feeding behaviour and detection of changes in the role of tardigrades along environmental gradients without the need of species identification.
Keywords:
želvušky; mikrofauna; Tardigrada; funkční vlastnosti; trofické skupiny; půdní potravní sítě
Available in the Digital Repository of University of South Bohemia.
The relationships among functional traits of tardigrades (Tardigrada), their diet, and environmental conditions
In this thesis, I explore several ways how to use functional traits to study the tardigrade role in the soil food web. The goal of the thesis was to show that it is possible to study tardigrade ...
Analýza slinných serpínů klíšťat Ixodes ricinus z hlediska strukturní biologie
KAŠČÁKOVÁ, Barbora
2022 - English
Znalost podrobné struktury proteinů a jejich komplexů s jinými proteiny, jako jsou například serpiny, pomáhá pochopit jejích mechanismus účinku. Serpiny, jako velká skupina proteázových inhibitorů mají téměř identické složení sekundární struktury a představují dokonalý příklad jak se dá vysvětlit jejich inhibičním proces prostřednictvím detailních strukturních analýz mnoha zástupců skupiny. Univerzální proces inhibice serpinu je znám a také je známo, že serpiny jsou strukturálně téměř identické zatímco funkčně rozmanité. Proto má každý serpin některé vlastnosti jemu specifické a znalost detailních serpinových struktur může vysvětlit vysokou funkční diverzitu. Rentgenová krystalografie byla a je jedním z nejběžnějších nástrojů používaných pro strukturní analýzu serpinu. Tato práce popisuje strukturní informace serpinů klíšťat Ixodes ricinus. Serpiny tohoto druhu jsou zodpovědné hlavně za modulaci imunitní odpovědi hostitele prostřednictvím inhibice zúčastněných proteáz. Serpiny s proteázami tvoří kovalentní komplexy. Tento proces vede k "sebevražednému" mechanismu, který inaktivuje jak proteázu tak i serpin. Zde jsou uvedeny výsledky rentgenové strukturní analýzy čtyř serpinů I. ricinus pojmenovaných: Iripin-3, Iripin-5, Iripin-4 a Iripin-1. Všechny pomáhají klíšťatům různými způsoby zůstat přichyceny k hostiteli po dostatečnou dobu pro krmení tím, že inhibují proteázy zapojené do imunitních obranných reakcí hostitele na kousnutí klíštětem. The knowledge of the detailed structure of proteins and their complexes with other proteins, such as serpins, helps to understand the mechanism of action. Serpins, a large protein group of protease inhibitors that possess almost identical secondary-structural folds, represent the perfect example of expanding the knowledge of their inhibition process through detailed structural analyses. The universal process of serpin inhibition is known, but also is known that serpins are structurally similar whereas their functional diversity is significant. Therefore, each serpin will have some properties specific to its own and knowledge of the serpin structures can explain high functional diversity. X-ray crystallography was one of the most common tools used for serpin structural analysis. This thesis describes the structural information of serpins found in Ixodes ricinus ticks. Serpins of this species are mainly responsible for the modulation of the host immune response via inhibiting involved proteases. Serpins with proteases form covalent complexes. This process leads to a suicide mechanism that inactivates the protease as well as serpin. Here are presented results of the X-ray structural analysis of four I. ricinus serpins named Iripin-3, Iripin-5, Iripin-4, and Iripin-1. All of them help the tick in different ways to stay attached to the host for sufficient time for feeding by inhibiting the proteases involved in host immune defense responses to a tick bite.
Keywords:
klíště; serpin; rentgenová krystalografie; Ixodes ricinus; sliny klíšťat; strukturní konformace
Available in the Digital Repository of University of South Bohemia.
Analýza slinných serpínů klíšťat Ixodes ricinus z hlediska strukturní biologie
Znalost podrobné struktury proteinů a jejich komplexů s jinými proteiny, jako jsou například serpiny, pomáhá pochopit jejích mechanismus účinku. Serpiny, jako velká skupina proteázových inhibitorů ...
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