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Imputation of missing genetic markers SNP
Kranjčevičová, Anita ; Přibyl, Josef (advisor) ; Jindřich, Jindřich (referee)
Working with genomic information in cattle breeding has become a standard procedure. This study is focused on completion of missing genetic markers - SNPs (single nucleotide polymorphisms) - on genetic chips. More specifically completion of missing values in datasets which contain pieces of information about SNP occurence in cattle genome. These polymorfisms are used for evaluation of genomic relationship, prediction of genomic breeding values and for the valuation of tested animals. The most common chips used for genotyping are Illumina and Affymetrix. Each company develops its own techniques of genotype obtaining. Affymetrix has unified coding type of SNPs among chips of different generations and thus even older data can be used. Illumina uses many coding types between different generations of chips. Thus, direct comparison of SNPs is not possible. Illumina has chips of different density and financial costingness. Illumina chips have become a standard all over the world and it is used by all breeding companies. The most used software programs for imputations are Beagle, AlphaImpute, Impute 2, FindHap, DAGPHASE, FImputePedImpute and MaCH. Each software requires a relationship between genotyped individuals. In common breeding business the genotyping is not in train of generations. That is why our own methodological process was used. The aim of this study is to map the current research about the completion of missing genetic markers on genetic chips and to verify the calculation process. In total, it was created 8 models with different amount of tested SNPs. From 10 to 100 neighbouring loci was tested. The testing was processed at chosen loci in two datasets. Dataset A contained 260 bull genotypes of different breeds from the Czech Republic. Dataset B contained 3982 genotypes of pure Holstein bulls from nine countries. In the first case a very good results were obtained. The prediction of missing values was almost accurate with model reliability 100%. The only exception was for almost entirely homozygous loci where the reliability reached only 55%. When the second dataset was tested, the most extensive model reached the reliability of 80 90% even in case of homozygous loci. The prediction error value was higher than in the first case. It was proven that missing values prediction is possible to calculate using the neighbouring SNPs. The outputs of this study are to be the base for further study of genomic data.
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Differencies of demographic development in CR
Pavlík, Jonáš ; Kába, Bohumil (advisor) ; Jindřich, Jindřich (referee)
This thesis analyze demographic development in several regions in years 1993 - 2014. The thesis describes the differences in demographic behavior between populations in this regions. Comparison is based on indicators of birth rate, mortality rate, marriage rate, divorce rate and migration.
First part is focused on theoretic description of demographic indicators nad methods which are used in statistical analysis. The second part contains the analysis itself based on the dates gained from Český statistický úřad. Prognosis of future development was calculated for indicators of marriage rate and divorce rate.
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Draft concept of a strategic plan for the municipality Obecnice
Šnajdrová, Radka ; Růžičková, Lenka (advisor) ; Jindřich, Jindřich (referee)
The dissertation is divided into theoretical part which is devoted to the description of regional development, strategic planning and a strategic plan comparison on the supranational scale, namely in selected European countries. The pratcical part describes the territory of the municipality Obecnice, its socio-econonic analysis in the field of economics, demographics, tourism, community facilities, infrastructure and the environment and local survey.
The dissertation result is analisis of general relations in the territory of the municipality Obecnice, synthesis of findings which is included in the municipality SWOT analysis and development measures formulation to achieve strategic visions. Outputs are in graphical, tabular and map expression. Since strategic planning is at several levels in the Czech Republic, the dissertation is dealing with local level only.
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Using of unseparated digestate as a phosphorus source for garden plants
Kujanová, Denisa ; Kulhánek, Martin (advisor) ; Jindřich, Jindřich (referee)
The advent of the modern trend of renewable resources was inevitable culmination of the development of civilization. Mankind learns more about use inexhaustible resources compared to depletion of reserves of non-renewable resources. Providers of renewable energy sources also include a biogas plant, which main function is the production of biogas. Biogas is produced in reactors by process of anaerobic fermentation without oxygen. As input for an agricultural biogas plants organic waste, cattle manure or for example energy grasses are used. The process of biogas production has the leftover of the fermentation at its end, so called digestate. Its composition depends especially on the inputs.
Digestate is a compound with high pH which is very rich not only for phosphorus but also for other nutrients. There are many studies dealing with the theory and practice of using digestate on the field for improving its properties and of other digestate usage. This diploma thesis has aim to explore combinations of unseparated digestate with peat and dolomite limestone with an effort to create a suitable substrate for different types of plants in terms of accessible phosphorus content.
During the experiment following plants were used between the years 2011 and 2015: Gazania rigens, Ocimum basilicum and Mentha piperita. For a control substrates following variants were used: Different types of commonly used growing substrates as the controls; peat combined with unseparated digestate in proportions of 5, 10, 15, 20, 25 % volume. In selected years dolomite limestone was also added in doses of 3, 6, 10, 15 g/l to stabilize pH.
The results of the work show a positive effect of the digestate on the substrate properties as for example pH value (with possible addition of limestone for stabilization) or dry matter. Digestate appears to be a suitable source of phosphorus for plants. In terms of the above-ground biomass yield of plants reached its maximum value at the control substrate Gramoflor. From the tested substrates it was in the most cases the substrate with 10 % digestate (in two years with doses of 6 a 15 g/l). Highest percentage of dry matter reached usually the control substrates.
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Funding of Health Care Service of Federal Republic of Germany
Adámková, Klára ; Stará, Dana (advisor) ; Jindřich, Jindřich (referee)
Financing healthcare is a problem not only in Germany but in many countries of Europe. Increasing total expenditure of health care resulted from many reasons, such as the aging population and the associated declining number of young people who contribute to the system. Another problem of financing health care, are ever increasing prices of medical devices, drugs, materials and energy. Since the beginning of the health system, Germany has been trying to stabilize the system through many reforms. The largest part of the revenues of the health system consists of contributions from members of statutory social insurance. Yet in Germany, financial participation in patients was implemented almost from the beginning of the health care system. Private costs are the second largest holder of health costs. Over the last 20 years, Germany has been among the countries that have a relatively balanced budget for financing health care. Among the most advanced countries in the world, which is seen in total expenditure of health care, had these expenses in recent years at around 11 percent of GDP.
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Project of a horse reproduction centre
Nágrová, Tereza ; Šichtař, Jiří (advisor) ; Jindřich, Jindřich (referee)
Due to the growing interest in the horse breeding and riding in recent years, the effort in their reproduction is also increasing. The process of equine reproduction leads to the improvement of the horse gene pool and better athletic performance. This is the reason why the artificial insemination methods were introduced besides a natural breeding, and the equine reproduction and the semen collection centers are build, as this biotechnological method requires the necessary equipment for the sampling, the evaluation and the processing of equine semen.
The aim of this master's thesis is to compose a summary of information about the necessary requirements for building an equine reproduction center and then develop a project of the specific equine reproduction center for the equestrian complex in Marienbad.
The review of literature provides general information about the building approval process, and technical requirements for agricultural buildings. In this part means for maintaining animal hygiene and veterinary measures are described as well as the requirements and minimum standards for horse stables, warehouses for feeding, bedding and paddocks. The next section focused on specific information about the approval process of the construction and the operation of an equine reproduction center, on the sanitary regulations, and the conditions for animal health surveillance and employees. Last but not least, this part of the thesis covers information about the requirements for technical equipment, the requirements for receiving and housing stallions. The majority of information is drawn from the laws and technical standards of the Czech Republic.
The following part is focused on the evaluation of the data sources. In this chapter the equestrian center in Marienbad, where the equine reproduction center will be built, is described along with all main activities of the whole complex, information about employees, about all the buildings and equipment and current breeding. These buildings, which will be rebuilt in order to be used for the construction of the equine reproduction center, are described in more detail.
The project itself begins with a business plan of the future reproduction center that analyzes an internal and an external business environment. The external environment is analyzed by competitors, suppliers and customers, and the internal environment is analyzed by marketing and HR strategy. Furthermore, the work is focused on the project itself, as all the buildings and parts of the reproductive center are described, for instance sampling room, laboratory, warehouse for insemination doses, stable for stallions, warehouse for feeding, paddocks and more. There is also a proposal for the necessary equipment and the economic evaluation of the reproductive center.
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Apoptotic changes in frozen-thawed ejaculate in stallions.
Bubeníčková, Filipa ; Šichtař, Jiří (advisor) ; Jindřich, Jindřich (referee)
The aim of the study was to evaluate the effect of incubation time, types of packaging , extenders and stallion´s individuality for the presence of apoptotic sperms after thawing insemination doses (ID).
The semen was collected from six Old Kladrubian stallions by standard collection method. Collected ejaculates were diluted with two extender types (GENT and LAKT) and filled into 0.5 ml straws and 5 ml aluminum tubes in which were frozen and stored in liquid nitrogen. The ID were evaluated for the presence of apoptotic sperm immediately after thawing (37 °C, 30 - 60 sec.) and after incubation 15, 30, 45 and 60 minutes after thawing using fluorochromes Yo-Pro 1, propidium iodide and fluorescence microscopy.
There was a statistically significant difference in the presence of apoptotic sperms in the ID diluted with different types of extender. In the ID frozen in Gent was higher number of apoptotic and apoptotic sperms from the total number of live cells. This results suggest a better survival rate of sperm in the extender Gent compared with lactate extender. It was shown the effect of packaging types for the presence of apoptotic sperms in the ID after thawing. Immediately after thawing there was statistically significantly higher average proportion of apoptotic spermatozoa in 5 ml tubes than in 0.5 ml straws. With incubation time the tests did not demonstrate any significant differences between different types of packaging. However, the percentage of apoptotic sperm cells from the total number of viable cells was higher in 0.5 ml straws. Nevertheless this difference was observed as statistically significant only after 1 hour incubation. When we compared the combination of the extender and the packaging type there were evident relevant differences. The common use of Gent and 5 ml tubes seems to give the best outcome.
The stallion´s individuality had significant effect on the presence of apoptotic sperms in cryopreserved ID. To increase the quality of produced ID it must be treated individually to each stallion, especially in case of the Old Kladrubian horse breed. High level of inbreeding can significantly affect semen quality and the success of reproduction.
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Podpora vývoje softwaru ve Visual Studiu 2005
Bezecný, Adam ; Kašparová, Alena (advisor) ; Jindřich, Jaroslav (referee)
Diplomová práce popisuje vývoj softvéru na platformě Visual Studio 2005 Team System (VSTS). Práce klade důraz především na popis funkcionality umožňující efektivní týmovou spolupráci a na popis nových inovativních rysů. Práce nepopisuje pouze pozitivní rysy produktu, identifikuje také základní nedostatky současné verze, na základě zkušeností vývojových týmů používajících VSTS a subjektivních názorech autora.
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