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The Analysis of Databases Suitable for IoT Environment
Kohout, Petr ; Vrána, Roman (referee) ; Kořenek, Jan (advisor)
In recent years, the volume of data stored in applications of all types has increased. As the volume of data grows, the demands on databases increase. The classic relational databases are no longer suitable. Therefore, it is switching to new, non-relational storage (called NoSQL). During this work, NoSQL databases focusing on processing large data volumes were analyzed and compared for their performance and system requirements. In addition, requirements for new sensor data storage for IoTCloud project were specified. Driver for database Cassandra was implemented and integrated into the IoTCLoud project.
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Identification of the Protein Tunnels Using Molecular Dynamics
Kohout, Petr ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
This thesis focuses on the analysis of protein structures. The aim is to design Caver Web 2.0 -- a new version of the web application that integrates additional scientific tools and allows users to go through a complicated workflow to provide relevant results without the need for a deeper knowledge of the integrated tools. Everything will be delivered through a simple and interactive user interface. The application extends the original Caver Web 1.0 application with new features. Caver Web 1.0 is a web server suitable for identifying protein tunnels and channels for which it allows to run ligand transport analyses. The program is characterized by an intuitive and user-friendly interface with minimum required input from the user. The server is suitable for researchers without advanced bioinformatics or technical knowledge. Its current version is well established and highly used in the scientific community (35,000 completed calculations in two years of operation). The most significant limitation of the current version is the ability to analyze only static structure, which often provides an incomplete biological picture. Therefore, it was decided to extend the tool to calculate molecular dynamics to provide a comprehensive picture of protein structure changes.
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Development of mycorrhizal communities in primary succession
Mádle, Jan ; Kohout, Petr (advisor) ; Ponert, Jan (referee)
Primary succession is the process of ecosystem development that takes place in sites that were not suitable for colonization by plants and organisms dependent on them. These sites arise either naturally, for example after a volcanic eruption or glacial retreat, or anthropogenically, for example by strip mining. During primary succession, plants colonise the bare substrate and gradually modify its abiotic and biotic conditions. During primary succession, interactions between plants and the soil microbiome, especially with fungi and bacteria, occur. Plants and soil microorganisms influence each other's growth and development through various interactions. Plants, or rather their roots, form a specific niche for a wide range of soil microbial communities. Through their roots, plants provide a wide range of substances, organic acids, sugars, amino acids and other often carbon-rich compounds that can serve as a substrate for microorganisms. Plants are able to do this by producing litter, root exudates, and translocation of sugars for symbiotic fungi and bacteria. Soil microorganisms contri- bute to the release of nutrients and the decomposition of organic materials that would otherwise be unavailable to plants. Many soil microorganisms can form a symbiotic relationship with the plant; this relationship may be...
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Role of exotic woody plant species in introductions of non-native symbiontic fungi
Vlk, Lukáš ; Kohout, Petr (advisor) ; Bárta, Jiří (referee) ; Anthony, Mark (referee)
The introduction of alien microorganisms so far received much less attention compared to macroorganisms. The introduction of alien fungi is currently considered an important and understudied component of global environmental change. Outbreaks of alien fungal pathogens threaten native plant and animal communities and cause immense ecological and economic damage. The introduction of alien mycorrhizal fungi enables the invasion of their hosts and could significantly alter key ecosystem functions and the soil biogeochemistry of recipient ecosystems. Evidence suggests that the introduction of alien plants serves as a major pathway for the spread of alien fungi. The main goal of this dissertation was to significantly contribute to the understanding of the phenomenon of the introduction of alien fungi. Specifically, this work aims to (1) assess the difference in the strategy of the two most commonly introduced alien tree groups on a global scale, pines and eucalypts, to obtain suitable ECM fungal partners in new areas, (2) assess the prevailing ecology of alien ECM fungi on a global scale, and (3) determine the extent of the introduction of alien fungi associated with alien trees in the chateau parks of the Czech Republic and identify environmental factors that affect their relative abundance, richness...
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Drivers of ectomycorrhizal fungal species richness on large spatial scales
Petr, Andrej ; Kohout, Petr (advisor) ; Šímová, Irena (referee)
Ectomycorrhizal (EcM) fungi form mutualistic relationships with some woody gymnosperms and angiosperms that play an important role in the functioning of most terrestrial ecosystems. Using enzymes capable of sequestering nitrogen and phosphorus from complex organic compounds, EcM fungi make these elements available to their host plants, which in turn provide them with the carbon compounds on which EcM fungi are vitally dependent. However, different species of EcM fungi differ from each other in their ability to sequester nitrogen and phosphorus from organic compounds, as well as in their carbon requirements from plants. The importance of the EcM symbiosis for the ecosystem therefore depends on the species richness of the EcM fungi, which is influenced at large spatial scales by a number of interacting factors, in particular the density and diversity of host plants, climate and soil properties. As EcM fungi generally exhibit low host preference, the density of host vegetation and the associated higher nutrient availability for EcM fungi has a greater influence on their species richness on a global scale than the phylogenetic diversity of host plants. In addition to these environmental factors, however, the distribution of EcM fungi is strongly related to their biogeographic history. In the context of...
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The effect of alien mycorrhizal plants on the community composition of mycorrhizal fungi
Kubove, Eva ; Kohout, Petr (advisor) ; Kolaříková, Zuzana (referee)
Among the most significant changes in biotic conditions is the globalization of the biosphere and the moving of organisms to their non-native range, which affects the local biocenosis and poses a threat to both the ecological and economic prosperity. Since mycorrhizal plants include most species, an important aspect that the plant must deal with when introducing and colonizing new territories is mycorrhizal symbiosis. This association, along with the composition of the symbiotic fungal community, can change in dynamic process, often in the negative way. Invasive plants disrupt the symbiosis with their allelopathic substances, dicrease the abundance of mycorrhizal fungi and host fitness. Also, they can take over the symbionts of native plants or change their community. When they gain monodominance in the community, they can change the dynamics of the entire ecosystem. This thesis aims to characterize and describe the role of mycorrhizae in plant invasions and the influence of these plants on the community composition of the mycorrhizal microbiome.
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The mycobiomes of vegetative organs of the dominant Mediterranean seagrass Posidonia oceanica (Posidoniaceae, Alismatales)
Soperová, Beáta ; Vohník, Martin (advisor) ; Kohout, Petr (referee)
Posidonia oceanica is a dominant seagrass of the Mediterranean Sea and its mycobiome has been increasingly studied, especially in recent years. Dozens of fungi associated with roots, rhizomes or leaves have been already described, but studies on the mycobiome of leaf sheaths are completely absent. One of the root-associated mycobionts is Posidoniomyces atricolor, which has not yet been isolated from any other organ. This thesis attempted to describe the mycobiome of vegetative organs of P. oceanica using two different methodological approaches - microscopic observation and molecular analyses. Microscopic observation confirmed the presence of fungal colonization in all vegetative organs except leaves. The conclusions from the microscopic part were subsequently verified by isolating and identifying several different endomycobionts, including P. atricolor, which has been also isolated for the first time from rhizomes and leaf sheaths. Leaf sheath mycobiome was then described for the first time ever.
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Identification of the Protein Tunnels Using Molecular Dynamics
Kohout, Petr ; Martínek, Tomáš (referee) ; Musil, Miloš (advisor)
This thesis focuses on the analysis of protein structures. The aim is to design Caver Web 2.0 -- a new version of the web application that integrates additional scientific tools and allows users to go through a complicated workflow to provide relevant results without the need for a deeper knowledge of the integrated tools. Everything will be delivered through a simple and interactive user interface. The application extends the original Caver Web 1.0 application with new features. Caver Web 1.0 is a web server suitable for identifying protein tunnels and channels for which it allows to run ligand transport analyses. The program is characterized by an intuitive and user-friendly interface with minimum required input from the user. The server is suitable for researchers without advanced bioinformatics or technical knowledge. Its current version is well established and highly used in the scientific community (35,000 completed calculations in two years of operation). The most significant limitation of the current version is the ability to analyze only static structure, which often provides an incomplete biological picture. Therefore, it was decided to extend the tool to calculate molecular dynamics to provide a comprehensive picture of protein structure changes.
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Significance of mycorrhizal symbiosis in invasiveness of Pinus strobus
Antl, Tomáš ; Kohout, Petr (advisor) ; Baláž, Milan (referee)
6 Abstract This study aimed to compare the mycorrhizal fungal communities inhabiting the roots of invasive Pinus strobus L. and native Pinus sylvestris L. We also compared carbon allocation into ectomycorrhizal fungal (EcMf) and other structures of the two pine species. The aim was to assess the influence of mycorrhiza on the invasive potential of P. strobus in the protected areas of National Park Bohemian Switzerland. The two field experiments were conducted on three locations of each species. We estimated the EcM extramatrical mycelium (EMM) production by measuring the ergosterol content in sterile sand filled mesh-bags. Next measured variables were: biomass of ectomycorrhizal and saprotrophic sporocarps, fine roots biomass and leaf litter biomass to compare the one season production of each measured variables. The results revealed a major difference in EcM sporocarps production, whereas on the P. sylvestris sites was the production 100% higher. Same results came from the fine roots measurements: P. sylvestris had a higher fine roots production, which may be also related with the production of EMM, which was about 60% higher as well. The EcMf species richness on the P. strobus root-tips was as high as the native pine, but the species composition was different. The P. strobus prefers EcMf species with...
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