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Development of DiCre parental lineage of \kur{Babesia divergens }
REICHENSDÖRFEROVÁ, Dominika
2022 - anglický
Babesia divergens is a tick-transmitted parasite of the order Piroplasmida, an important causative agent of bovine and human babesiosis. Even though Babesia represent an important worldwide veterinary threat and an emerging risk to humans, some of the fundamental principles of their parasitic lifestyle are still poorly understood. One of the approaches, which help us to better understand the biology of Babesia parasites and their interaction with hosts or vectors, is functional genomics. Hence, the aim of this thesis is to establish a DiCre parental lineage of B. divergens that may provide the absent genome editing technique of conditional gene knock-out. Such a tool will help to functionally characterize essential genes/proteins and validate them as novel targets for the yet missing specific treatment. We have selected and identified an eligible recipient locus in the B. divergens genome into which a DiCre cassette will be integrated via homology recombination. We have validated and determined the optimal concentration of WR99210 and G-418 for their use as selection markers for transfected B. divergens cultures. Finally, we have designed and constructed the plasmid vector containing the DiCre cassette for the generation of DiCre parental B. divergens lineage that may be universally applicable to functionally validate any genes/proteins of interest. Babesia divergens is a tick-transmitted parasite of the order Piroplasmida, an important causative agent of bovine and human babesiosis. Even though Babesia represent an important worldwide veterinary threat and an emerging risk to humans, some of the fundamental principles of their parasitic lifestyle are still poorly understood. One of the approaches, which help us to better understand the biology of Babesia parasites and their interaction with hosts or vectors, is functional genomics. Hence, the aim of this thesis is to establish a DiCre parental lineage of B. divergens that may provide the absent genome editing technique of conditional gene knock-out. Such a tool will help to functionally characterize essential genes/proteins and validate them as novel targets for the yet missing specific treatment. We have selected and identified an eligible recipient locus in the B. divergens genome into which a DiCre cassette will be integrated via homology recombination. We have validated and determined the optimal concentration of WR99210 and G-418 for their use as selection markers for transfected B. divergens cultures. Finally, we have designed and constructed the plasmid vector containing the DiCre cassette for the generation of DiCre parental B. divergens lineage that may be universally applicable to functionally validate any genes/proteins of interest.
Klíčová slova:
B. divergens; DiCre cassette; DiCre parental B. divergens lineage; treatment; Gibson assembly
Plné texty jsou dostupné v digitálním repozitáři JČU.
Development of DiCre parental lineage of \kur{Babesia divergens }
Babesia divergens is a tick-transmitted parasite of the order Piroplasmida, an important causative agent of bovine and human babesiosis. Even though Babesia represent an important worldwide veterinary ...
Calculation of vibrational SFG spectra from molecular dynamics simulations
MUSIL, Patrik
2022 - anglický
In this thesis, implementation of calculation vibrational Sum-Frequency Generation (SFG) spectra from classical molecular simulations of aqueous solutions in the O-H vibrations region is presented. The key part of the thesis was significant improvement of the original codes used by the group of Prof. Marie-Pierre Gaigeot to post-process ab initio molecular dynamics trajectories to predict vibrational SFG spectra and apply it to classical molecular dynamics simulations. Particular attention was paid to modifying and optimizing the code for processing much larger systems (number of molecules) and much longer trajectories (longer simulation times), allowing to take advantage of classical simulations to work on larges scales than the ab initio simulations. The code also integrates calculations of contributions from water O-H bonds and surface hydroxyls. As a new feature, calculation of cross-correlations among molecules was implemented. The performance of the resulting codes is verified and the influence of classical molecular simulation parameters, as well as parameters entering the SFG spectra calculations, on the calculated vibrational SFG spectra is studied for fluorite/water interface. In this thesis, implementation of calculation vibrational Sum-Frequency Generation (SFG) spectra from classical molecular simulations of aqueous solutions in the O-H vibrations region is presented. The key part of the thesis was significant improvement of the original codes used by the group of Prof. Marie-Pierre Gaigeot to post-process ab initio molecular dynamics trajectories to predict vibrational SFG spectra and apply it to classical molecular dynamics simulations. Particular attention was paid to modifying and optimizing the code for processing much larger systems (number of molecules) and much longer trajectories (longer simulation times), allowing to take advantage of classical simulations to work on larges scales than the ab initio simulations. The code also integrates calculations of contributions from water O-H bonds and surface hydroxyls. As a new feature, calculation of cross-correlations among molecules was implemented. The performance of the resulting codes is verified and the influence of classical molecular simulation parameters, as well as parameters entering the SFG spectra calculations, on the calculated vibrational SFG spectra is studied for fluorite/water interface.
Klíčová slova:
computer simulations; solid-liquid interface; nonlinear optics; sum-frequency generation; spectroscopy
Plné texty jsou dostupné v digitálním repozitáři JČU.
Calculation of vibrational SFG spectra from molecular dynamics simulations
In this thesis, implementation of calculation vibrational Sum-Frequency Generation (SFG) spectra from classical molecular simulations of aqueous solutions in the O-H vibrations region is presented. ...
Analysis of the dicyemid diversity using amplicon sequencing
FLEGROVÁ, Tereza
2022 - anglický
Using amplicon sequencing, this study reveals dicyemid diversity around the world as well as within individual cephalopod hosts. A wide number of samples of multiple species were collected to reflect true dicyemid diversity. Heterogeneity primers were designed in order to improve the sequencing performance of the Illumina platform. A complex bioinformatic pipeline was implemented to process non-overlapping reads. The species delimitation methods were used to categorize occurring dicyemid types. Using the output of implemented methods, dicyemid diversity was assessed, proposing new trends opposing the current methodology.
Klíčová slova:
amplikonové sekvenování; dicyemida; populační diverzita; illumina
Plné texty jsou dostupné v digitálním repozitáři JČU.
Analysis of the dicyemid diversity using amplicon sequencing
Using amplicon sequencing, this study reveals dicyemid diversity around the world as well as within individual cephalopod hosts. A wide number of samples of multiple species were collected to reflect ...
mTOR-regulated translation during first the wave of inner cell generation in mouse preimplantation embryos
ČERNÁ, Pavlína
2022 - anglický
The aim of this master thesis was to investigate the role of mTOR and connected pathways in early mouse preimplantation development. The aim of this master thesis was to investigate the role of mTOR and connected pathways in early mouse preimplantation development.
Klíčová slova:
mouse preimplantation development; trophectoderm; primitive endoderm; epiblast; mTOR signalling pathway
Plné texty jsou dostupné v digitálním repozitáři JČU.
mTOR-regulated translation during first the wave of inner cell generation in mouse preimplantation embryos
The aim of this master thesis was to investigate the role of mTOR and connected pathways in early mouse preimplantation development....
Bacterial life history strategies in gamma-irradiated arable soil receiving different microbial inocula
FARKOVÁ, Karolína
2022 - anglický
Půda obsahuje mimořádnou úroveň mikrobiální biodiverzity, která podporuje klíčové funkce ekosystému. Pochopení toho, jak se půdní mikrobiální společenstva v zemědělských ekosystémech utvářejí a jaké vlastnosti vykazují (tj. jaké funkce a služby zprostředkovávají), je nezbytné pro lepší předvídání důsledků ztráty biologické rozmanitosti. Tato práce analyzuje složení, diverzitu a životní strategie půdních bakteriálních společenstev po zavedení mikrobiálních společenstev z různých zdrojů (tj. půdy a kravských exkrementů) do sterilní půdy (ozářené -zářením). Výsledky ukazují, že bakterie z půdy a exkrementů se v -ozářené půdě úspěšně etablovaly a že složení a diverzita bakteriálních společenstev silně závisí na zdroji inokulace. Analýzy vybraných funkčních znaků prokázaly, že taxony časných kolonizátorů se vyznačovaly vyšším počtem kopií genu 16S rRNA, menšími genomy a zvýšenou pohyblivostí a schopností sporulace než původní půdní bakteriální společenstva. Kromě toho, přestože půdy vykazovaly podobné počáteční fyzikálně-chemické a biochemické vlastnosti, různá mikrobiální společenstva vytvářela podstatné rozdíly ve vlastnostech půdy a mikrobiálně zprostředkovaných funkcích. Tato práce přispívá k lepšímu pochopení toho, jak je složení bakteriálního společenstva důležité pro mikrobiální biodiverzitu v půdě a jak naopak může biodiverzita přispívat ke změnám půdní úrodnosti a aktivity bakterií prostřednictvím různých životních strategií a vlastností. Soil contains an extraordinary level of microbial biodiversity that supports key ecosystem functions. Understanding how soil microbial communities assemble in agricultural ecosystems, as well as what traits they exhibit (i.e., what functions and services they mediate), is essential to better predict the consequences of biodiversity loss. This thesis analyzes the composition, diversity, and life history strategies of soil bacterial communities after the introduction of microbial communities from different sources (i.e., soil and cow excreta) into sterile soil (-irradiated). The results show that bacteria from soil and excreta successfully established in the -irradiated soil and that the bacterial composition and diversity strongly depends on the inoculation source. Analyses of selected functional traits proved that early colonizer taxa were characterized by having higher 16S rRNA copy numbers, smaller genomes and elevated motility and sporulation abilities than the original soil bacterial community. In addition, despite the soils showing similar initial physicochemical and biochemical properties, the different bacterial assemblages generated strong differences in soil properties and microbially-mediated functions. This thesis contributes to a better understanding on how the composition of microbial community is important for the microbial biodiversity in soil and in turn, how biodiversity can contribute to changes in soil fertility and bacterial activity through different life history strategies and traits.
Klíčová slova:
půda; bakteriální komunita; funkční znaky; životní strategie; zemědělství
Plné texty jsou dostupné v digitálním repozitáři JČU.
Bacterial life history strategies in gamma-irradiated arable soil receiving different microbial inocula
Půda obsahuje mimořádnou úroveň mikrobiální biodiverzity, která podporuje klíčové funkce ekosystému. Pochopení toho, jak se půdní mikrobiální společenstva v zemědělských ekosystémech utvářejí a jaké ...
Subcellular insight into cholesterol-mediated proliferation of the tick cell line
KROPÁČKOVÁ, Sára
2022 - anglický
Arthropods, including ticks, are not able to synthetise cholesterol de novo. However, cholesterol is an essential component of their cell membranes and serves as a precursor for the synthesis of steroid hormones. In this thesis, I looked at the biological function of exogenous cholesterol on the tick Ixodes ricinus cell line IRE/CTVM19. I verified the need for cholesterol supplementation in the growth medium for proper cell proliferation. Cellular proliferation was stimulated by cholesterol and not by other sterols (ergosterol, sitosterol). We further explored the two assumed aforementioned cholesterol cellular roles, but also investigated the role of cholesterol as a signal molecule: The effect of cholesterol sensing is described on the tick cell level, as well as on the level of the whole organism, using the ex vivo feeding system of ticks. This work provides novel insights into the cholesterol biology of ticks and tick cells, increasing our understanding of tick-host blood molecules' interaction. Arthropods, including ticks, are not able to synthetise cholesterol de novo. However, cholesterol is an essential component of their cell membranes and serves as a precursor for the synthesis of steroid hormones. In this thesis, I looked at the biological function of exogenous cholesterol on the tick Ixodes ricinus cell line IRE/CTVM19. I verified the need for cholesterol supplementation in the growth medium for proper cell proliferation. Cellular proliferation was stimulated by cholesterol and not by other sterols (ergosterol, sitosterol). We further explored the two assumed aforementioned cholesterol cellular roles, but also investigated the role of cholesterol as a signal molecule: The effect of cholesterol sensing is described on the tick cell level, as well as on the level of the whole organism, using the ex vivo feeding system of ticks. This work provides novel insights into the cholesterol biology of ticks and tick cells, increasing our understanding of tick-host blood molecules' interaction.
Klíčová slova:
tick; cholesterol; tick cell line; IRE/CTVM19; Hedgehog signalling pathway
Plné texty jsou dostupné v digitálním repozitáři JČU.
Subcellular insight into cholesterol-mediated proliferation of the tick cell line
Arthropods, including ticks, are not able to synthetise cholesterol de novo. However, cholesterol is an essential component of their cell membranes and serves as a precursor for the synthesis of ...
Numerical simulations of dynamic processes in the solar corona
BELOV, Sofya
2022 - anglický
This master's thesis deals with 3D numerical simulations of turbulent flow past magnetic structures in the solar corona, focusing on the phenomenon of vortex shedding. This phenomenon is well known in hydrodynamic conditions. Still, it has not yet been satisfactorily investigated in magnetohydrodynamic (MHD) conditions, such as in the solar atmosphere, where its occurrence has been suggested by several studies and may explain some oscillatory phenomena. Numerical code Lare3d is used for the simulations.
Klíčová slova:
vortex shedding; solar corona; coronal loops; solar prominences; coronal mass ejections; kink oscillations; magnetohydrodynamics; numerical simulations; Lare3d
Plné texty jsou dostupné v digitálním repozitáři JČU.
Numerical simulations of dynamic processes in the solar corona
This master's thesis deals with 3D numerical simulations of turbulent flow past magnetic structures in the solar corona, focusing on the phenomenon of vortex shedding. This phenomenon is well known in ...
The role of Q tRNA modification in codon biased translation in \kur{Leishmania mexicana}
ŠVÁBOVÁ, Monika
2022 - anglický
The aim of the thesis was to standardize polysome profiling and ribosome profiling protocols for the parasitic protist Leishmania mexicana in order to identify the effect of Q-tRNAs in translation. In addition, we analyzed the role of queuosine (Q) t-RNA modification in the cell cycle of L. mexicana. The proteomics analysis was carried out in order to elucidate the role of Q-tRNAs in protein folding.
Klíčová slova:
Leishmania mexicana; translation; queuosine; modification; ribosome profiling; polysome profiling; tRNA
Plné texty jsou dostupné v digitálním repozitáři JČU.
The role of Q tRNA modification in codon biased translation in \kur{Leishmania mexicana}
The aim of the thesis was to standardize polysome profiling and ribosome profiling protocols for the parasitic protist Leishmania mexicana in order to identify the effect of Q-tRNAs in translation. In ...
Analysis of genetic diversity of \kur{Borrelia burgdorferi} sensu lato and \kur{Borrelia miyamotoi} across Central and Eastern Europe using multilocus sequence typing (MLST) in range of Slovakia and data from the MLST database with focus on Central and Eastern Europe
MORÁVKOVÁ, Veronika
2022 - anglický
The study was based on tick collection, DNA extraction, PCR amplification, sequencing and computational analyses of Borrelia burgdorferi sensu lato and B. miyamotoi. The study included evaluation on the prevalence of Borrelia burgdorferi sensu lato and B. miyamotoi in Ixodes ricinus ticks across the Slovak Republic based on the collection of ticks from 2017. The spirochetes were further classified into genospecies as well as sequence types (ST) according to MLST method by amplifying and sequencing eight housekeeping genes. Subsequently, population-genetic relationships of Borrelia tick-borne pathogens across Central and Eastern Europe were analysed. The study was based on tick collection, DNA extraction, PCR amplification, sequencing and computational analyses of Borrelia burgdorferi sensu lato and B. miyamotoi. The study included evaluation on the prevalence of Borrelia burgdorferi sensu lato and B. miyamotoi in Ixodes ricinus ticks across the Slovak Republic based on the collection of ticks from 2017. The spirochetes were further classified into genospecies as well as sequence types (ST) according to MLST method by amplifying and sequencing eight housekeeping genes. Subsequently, population-genetic relationships of Borrelia tick-borne pathogens across Central and Eastern Europe were analysed.
Klíčová slova:
Borrelia afzelii; Borrelia garinii; Borrelia burgdorferi sensu stricto; Borrelia miyamotoi; PCR; MLST; MLSA; Ixodes ricinus; sequence type; genetic diversity; Slovak Republic; Slovakia; population-genetic analysis; Lyme borreliosis; Lyme disease; relapsing fever
Plné texty jsou dostupné v digitálním repozitáři JČU.
Analysis of genetic diversity of \kur{Borrelia burgdorferi} sensu lato and \kur{Borrelia miyamotoi} across Central and Eastern Europe using multilocus sequence typing (MLST) in range of Slovakia and data from the MLST database with focus on Central and Eastern Europe
The study was based on tick collection, DNA extraction, PCR amplification, sequencing and computational analyses of Borrelia burgdorferi sensu lato and B. miyamotoi. The study included evaluation on ...
Svalbard reindeer and its interaction with extreme polar environment
KAVANOVÁ, Veronika
2022 - anglický
Two distinct populations of Svalbard reindeer are compared based on their antler parameters. Relative antler size and number of tines are supposed to reflect well environmental conditions of the sedentary population within the growing season. Both studied populations are well spatially isolated due to high mountain ridges, glaciers and fjords. The population in Petuniabukta occupies sparsely vegetated region with harsh climatic conditions, whereas Skansbukta represents area with continuous tundra vegetation, milder climatic conditions and consequently also longer vegetation season. These environmental factors probably lead to significant differences in relative antler size and number of tines. Skansbukta population has larger relative antler size and higher number of tines than the population in Petuniabukta. Two distinct populations of Svalbard reindeer are compared based on their antler parameters. Relative antler size and number of tines are supposed to reflect well environmental conditions of the sedentary population within the growing season. Both studied populations are well spatially isolated due to high mountain ridges, glaciers and fjords. The population in Petuniabukta occupies sparsely vegetated region with harsh climatic conditions, whereas Skansbukta represents area with continuous tundra vegetation, milder climatic conditions and consequently also longer vegetation season. These environmental factors probably lead to significant differences in relative antler size and number of tines. Skansbukta population has larger relative antler size and higher number of tines than the population in Petuniabukta.
Klíčová slova:
Svalbard reindeer; antlers; population characteristics; environmental conditions
Plné texty jsou dostupné v digitálním repozitáři JČU.
Svalbard reindeer and its interaction with extreme polar environment
Two distinct populations of Svalbard reindeer are compared based on their antler parameters. Relative antler size and number of tines are supposed to reflect well environmental conditions of the ...
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