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Methods for class prediction with high-dimensional gene expression data
Šilhavá, Jana ; Matula, Petr (referee) ; Železný, Filip (referee) ; Smrž, Pavel (advisor)
Dizertační práce se zabývá predikcí vysokodimenzionálních dat genových expresí. Množství dostupných genomických dat významně vzrostlo v průběhu posledního desetiletí. Kombinování dat genových expresí s dalšími daty nachází uplatnění v mnoha oblastech. Například v klinickém řízení rakoviny (clinical cancer management) může přispět k přesnějšímu určení prognózy nemocí. Hlavní část této dizertační práce je zaměřena na kombinování dat genových expresí a klinických dat. Používáme logistické regresní modely vytvořené prostřednictvím různých regularizačních technik. Generalizované lineární modely umožňují kombinování modelů s různou strukturou dat. V dizertační práci je ukázáno, že kombinování modelu dat genových expresí a klinických dat může vést ke zpřesnění výsledku predikce oproti vytvoření modelu pouze z dat genových expresí nebo klinických dat. Navrhované postupy přitom nejsou výpočetně náročné. Testování je provedeno nejprve se simulovanými datovými sadami v různých nastaveních a následně s~reálnými srovnávacími daty. Také se zde zabýváme určením přídavné hodnoty microarray dat. Dizertační práce obsahuje porovnání příznaků vybraných pomocí klasifikátoru genových expresí na pěti různých sadách dat týkajících se rakoviny prsu. Navrhujeme také postup výběru příznaků, který kombinuje data genových expresí a znalosti z genových ontologií.
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Optimization of network flow monitoring
Žádník, Martin ; Lhotka,, Ladislav (referee) ; Matoušek, Radomil (referee) ; Sekanina, Lukáš (advisor)
The thesis deals with optimization of network flow monitoring. Flow-based network traffic processing, that is, processing packets based on some state information associated to the flows which the packets belong to, is a key enabler for a variety of network services and applications. The number of simultaneous flows increases with the growing number of new services and applications. It has become a challenge to keep a state per each flow in a network device processing high speed traffic. A flow table, a structure with flow states, must be stored in a memory hierarchy. The memory closest to the processing is known as a flow cache. Flow cache management plays an important role in terms of its effective utilization, which affects the performance of the whole system. This thesis focuses on an automated design of cache replacement policy optimized to a deployment on particular networks. A genetic algorithm is proposed to automate this process. The genetic algorithm generates and evaluates evolved replacement policies by a simulation on obtained traffic traces. The proposed algorithm is evaluated by designing replacement policies for two variations of the cache management problem. The first variation is an evolution of the replacement policy with an overall low number of state evictions from the flow cache. The second variation represents an evolution of the replacement policy with a low number of evictions belonging to large flows only. Optimized replacement policies for both variations are found while experimenting with various encoding of the replacement policy and genetic operators. The newly evolved replacement policies achieve better results than other tested policies. The evolved replacement policy lowers the overall amount of evictions by ten percent in comparison with the best compared policy. The evolved replacement policy focusing on large flows lowers the amount of their evictions two times. Moreover, no eviction occurs for most of the large flows (over 90%). The evolved replacement policy offers better resilience against flooding the flow cache with large amount of short flows which are typical side effects of scanning or distributed denial of service activities. An extension of the replacement policy is also proposed. The extension complements the replacement policy with an additional information extracted from packet headers. The results show further decrease in the number of evictions when the extension is used.
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(Arbo)viruses in high European Arctic
ELSTEROVÁ, Jana
Since an ongoing climate change covers strongly the polar areas. Higher temperatures and related climate parameters bring the emergence of new parasites and their pathogens to higher latitudes. This may influence zoonotic diseases including arthropod-transmitted diseases. The tick species Ixodes uriae, parasitizing seabirds in the Arctic, may transmit many pathogens including various arboviruses, Borrelia spirochetes and Babesia apicomplexans. In the study we diagnosed 89 individuals of seabird tick Ixodes uriae and searched for arthropod-borne viruses from the genera Flavivirus, Alphavirus, Orthobunyavirus, Phlebovirus and Orbivirus using genus-specific primers. Moreover we searched for presence of Borrelia spp. and Babesia spp. DNA in the ticks. All samples were negative after PCR amplification for all tested pathogens. The result signalizes that tested pathogens might not be present in such high latitudes of European Arctic. Though, the possibility of introduction of these pathogens may be observable in near future due to quick changing of the Arctic ecosystem with the rising of migration of vertebrate hosts including humans to the polar areas. It is though important to continue to study potential presence of pathogens in polar areas. We are working on increase of the number of tick samples to confirm the presence or absence of the tick-borne pathogens in the European Arctic.
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Is genetic diversity congruent with morphological diversity across the distributional range of the Melampyrum subalpinum group (Orobanchaceae)?
CHLUMSKÝ, Jan
Allozymes were used to assess the genetic structure of 27 populations of Melampyrum subalpinum group and an artificial pollination experiment was carried out to examine the possibility of autogamy. Genetic variation was generally congruent with the known morphological variation of the group. The results corresponded with the central-marginal concept. Allelic enrichment due to hybridization with M. nemorosum was observed in some Austrian populations. Czech and Slovak populations do not differ from Austrian populations. The high inbreeding coefficient and the pollination experiment do not contradict the possibility of autogamy.
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Adolescent overweight and obesity
JINDROVÁ, Kateřina
My bachelor´s thesis deal with obesity of adolescents and problems with overweight. These problems are described in details, and after that divided into specific parts. The main goal of my bachelor´s thesis is to chart problems with obesity and overweight in age group from 15 to 18 (adolescents) and primary describe their eating habits and physical activity. Theoretical part is focused on occurrence of overweight and obesity in the Czech Republic and in the world, causes of its origin, risk factors, classification and diagnosis, types, therapy and prevention. This bachelor´s work dealing with rational diet, describing basic principles of healthy catering and explaining right or wrong foodstuffs. I point mainly on prevention of overweight and obesity by healthy eating and physical activity. Methodical part is processed thanks to quantitative research. Data were gained by questionnaires, which were given to high school students (1st - 3rd grade). The research group contains 150 respondents from different schools in České Budějovice and close neighborhood. Final results are written down primary in graphs with commentary and data charts. In case of right use of qualitative research, there were determined two hypotheses. First hypothesis: Overweight and obesity is more occurred at adolescents with wrong eating habits. Second hypothesis: Overweight and obesity is more occurred at adolescents with low physical activity. For developing exploratory part, there was used quantitative research, which was provided by questionnaires given to students of age from 15 to 18. Entire data were processed by the use of program Microsoft Excel, and its calculations and functions. The answers of respondents were registered into database, and, by using specific excel functions, I was able to report data in determined categories. The research was mainly concentrated on physical activity and eating habits. Final results are put into well-arranged graphs, which are always enriched by comments, eventually completed by data tables, and, subsequently, statistically evaluated. In results, there might be seen two main differences between adolescents with standard weight and adolescents with overweight or obesity problems. One of those is irregularity in eating and wrong eating habits; big difference is also proved in physical activity. Adolescents with obesity or overweight have often irregular food intake, they drink a lot of high caloric beverages such as Coca-Cola, Sprite, Fanta etc., deficient income of fruit, vegetables, legumes, fish, or low physical activity. Only few of obese adolescents is different, because their problem is caused genetically. Adolescents with standard weight eat more regularly, but there are also some special cases, who have similarly wrong eating habits as obese people; however, all of these adolescents have one typical quality regular physical activity. Both hypotheses are confirmed. The results show that obesity is mainly caused by genetic predispositions, but these factors can be positively affected by periodic physical activity or appropriate eating habits. At the end of the thesis, it should be mentioned that it is necessary to be focused on right eating habits and regular physical from the very young age, when the basic customs and habits are assumed. That should include parents' action around their children, as they are usually the first example and they have the biggest influence.It is important to develop knowledge about all kinds of prevention, which are in most cases major in defending against formation of overweight and obesity.
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The effect of pyrethroid based pesticides on fish
RICHTEROVÁ, Zuzana
Pyrethroids are ones of the most used pesticides worldwides. The widespread use and high stability of pyrethroids lead to the assumption of that their occurrence in the environment could be quite frequent. They can reach water ecosystem as pollutants. Residues of pyrethroids are not only detected in the water column, but also in sediments and in fish tissues. The first study was devoted to the product Nexide containing 60 g.l-1 of active substance gamma-cyhalothrin. Tested Nexide concentrations were 5, 25, 50, 100, and 250 µg.l-1. Early life stage test was used.Common carp (Cyprinus carpio) was tested. There were significant mortalities in all concentrations except the lowest concentration during the trial. The lowest concentration tested 5 µg.l-1 only caused a slightly increased mortality. This lowest concentration influenced the growth in length and weight negatively, decelerated ontogenetic development, and made the body surface of the individuals darker. Histopathology of individuals from this concentration revealed dystrophy in liver. Examination of kidney, intestine and gills did not show significant histopathological differences compared with control. The evaluation of selected parameters of oxidative stress demonstrated a significantly higher activity of detoxification enzyme glutathione-S.transferase (GST) and a significantly lower activity of defensive enzyme glutathione peroxidase (GPx) compared with the control group. The other examined parameters of oxidative stress such as catalase (CAT), glutation reductase (GR), and lipid peroxidation determined by using the thiobarbituric acid-reactive substances (TBARs) were comparable to the control group. Changes in oxidative stress parameters suggest that exposure of the organism to the product Nexide in the given concentration leads to dysbalance of defensive enzymes. The second study was devoted to the product Cyperkill 25 EC containing 250 g.l-1. Tested Cyperkill 25 EC concentrations were 7.2, 36, 72, 144, and 360 µg.l-1. The procedure of the trial was the same as the preceded one. There were 100% mortalities in all concentrations except the lowest concentration during the trial. The lowest tested concentration 7.2 µg.l-1 allowed 90% of individuals to stay alive till the end of experiment. The lowest concentration influenced the growth in length and weight negatively and decelerated ontogenetic development compared with the control. Any individual exposed to this concentration did not reach juvenile stage until the end of the trial. Dark pigmentation was visible in 68% of these exposed individuals on the last day. Similar darkening was visible in individuals from higher concentrations shortly before death too. Histological examination did not revealed significant changes in intestine, liver, kidney, and gills compared with the control group. Evaluation of selected parameters of oxidative stress demonstrated significantly lower activities of GST, GR, and GPx. Activities of CAT and TBARS were comparable with the control group. Changes in oxidative stress parameters suggest that exposure of the organism to the product Cyperkill 25 EC in the given concentration could induce oxidative stress and interfere with the activities of antioxidant enzymes. The presented thesis summarises actual data about pyrethroids and their influence on fish. The demonstrated effects confirm high susceptibility of early developmental stages of fish to tested pesticides. When interpreting the results, we have to take into account the fact that studies showed this risk even on single pyrethroid substances. But water organisms are exposed to many other more or less toxic products and substances in a real environment. These xenobiotics could react with each other and their mixture could even potentiate negative effects. The performed studies also clearly show the significant differences in the sensitivity of embryonic and embryolarval tests.
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Iniciace pohybu byčíku, signalizace a regulace pohyblivosti spermií ryb: fyzikální a biochemické řízení
PROKOPCHUK, Galina
The current study attempted to shed light on the regulatory processes and response arrangements of fish spermatozoa during the course of maturation and motility initiation. The first intent of this study was to improve the understanding of the mechanism underlying the acquisition of potential for sperm motility in sturgeon. Up to present work, the physiological process underlying sperm maturation in this species has not been described at all. Our results showed that sperm maturation in sturgeon occurs outside the testes because of dilution of sperm by urine and involves the participation of high molecular weight substances as well as calcium ions present in seminal fluid and/or urine. The second aim of the present study was to investigate the coping mechanisms in fish spermatozoa with osmotic and ionic activating mode, as well as in spermatozoa of euryhaline fishes, to various environmental conditions. We showed that alteration of environmental osmolality might affect the fish sperm in different ways, depending on fish species and modes of spermatozoa motility activation either osmotic or ionic mode. In response to osmotic stress caused by hypotonicity, carp spermatozoa regulated the flow of water across their cell membrane and increased their cytoplasmic volume during their short motility period. In contrast, no indications of sperm volume changes were observed neither in sterlet nor in brook trout spermatozoa, both of which having an ionic mode of motility activation. We also examined the mechanism by which sperm motility triggering in euryhaline fishes can adapt to a broad range of environmental salinity. Our results demonstrated that spermatozoa of euryhaline tilapia, Sarotherodon melanotheron heudelotii, reared in fresh-, sea- or hypersaline water can be activated in hypotonic, isotonic or hypertonic conditions of swimming milieu, provided Ca2+ ions are present at various levels. It was established that the higher the fish rearing salinity or the more hypertonic ambient media at spermatozoa activation, the higher extracellular concentration of Ca2+ ions is required. The results obtained in the present study allow suggesting that osmolality is not the main factor inhibiting sperm motility inside the testis in the S. melanotheron heudelotii. A third aim of this study was investigation of the regulation of motility initiation process and description of flagellar beating initiation in chondrostean spermatozoa. We detected that K+ inhibition of sperm motility in sturgeon can be by-passed due to the pre-exposure of sperm cells to a high osmolality shock prior to its transfer to K+-rich swimming media. Thus, we hypothesized that sturgeon spermatozoa may be activated by use of an unexpected signaling pathway, independent from regular ionic stimulation. The successive activation steps in sturgeon spermatozoa were investigated by high-speed video microscopy, using specific experimental situation, where sperm motility initiation was delayed in time up to several seconds. At motility initiation, the first couple of bends formed at the basal region begins to propagate towards the flagellar tip, but gradually fades when reaching the mid-flagellum. This behavior repeats several times until a stage where the amplitudes of bends gradually reach similar value, what eventually leads to sperm progressive displacement. The total period needed for the flagellum to switch from immobility with rigid shape to full activity with regular propagating bends ranges from 0.4 to 1.2 seconds. In conclusion, the results of the current study bring valuable pieces of information into the general understanding of the processes of maturation of fish spermatozoa, their adaptability to different physical and biochemical circumstances, the extra- and intra-cellular signaling as well as the regulatory mechanisms of motility activation in fish spermatozoa.
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The use of (nano)oxides for metal and metalloid stabilization in contaminated soils
Michálková, Zuzana ; Komárek, Michael (advisor) ; Luke, Luke (referee)
The main objective of the thesis was to evaluate the potential of selected Mn and Fe (nano)oxides for the stabilization of metals and metalloids in contaminated soils. The research was focused basically on three materials - commercial nanomaghemite (Fe III), nanomagnetite (Fe II,III) and a synthetic amorphous Mn oxide (AMO). The main aim of the work was to provide a complex view on the chosen stabilizing amendments regarding not just their direct influence on contaminants mobility and stabilization mechanisms, but also their stability and alterations in soil conditions together with influence on soil microorganisms and higher plants. Firstly, adsorption properties of the tested materials towards Cd, Cu, Pb and As were investigated. In this context, the most effective material showed to be the AMO reaching one to two orders of magnitude higher adsorption capacities than Fe III and Fe II,III under given experimental conditions. Interestingly, the rate of As(V) adsorption onto AMO was increasing with increasing pH as a result of high pHzpc of the AMO (8.1) and significant dissolution of this phase at lower pH values. As a next step, the influence of (nano)oxides on metal(loid)s mobility and other physico-chemical soil characteristics after application to contaminated soil was examined. Again, the AMO proved to be the most efficient in reducing mobile pools of Cd, Cu, Pb, Zn and As. On the other hand, Fe III and Fe II,III addition had generally less significant effects on contaminants mobility. AMO application further resulted in an increase of soil pH connected with AMO dissolution and unwanted decomposition of soil organic matter. When (nano)oxides alterations in soil conditions were observed, MnCO3 coatings were identified on AMO surface while no significant changes were recorded for Fe III and Fe II,III. As the MnCO3 formation was connected with increased AMO stability, AMO particles synthetically covered with MnCO3 coating (denoted as SM AMO) were prepared. Although the SM-AMO had a lower mass loss in soil than pure AMO, the stabilizing efficiency was almost the same for both materials. The differences in surface composition of both materials were decreasing with time as MnCO3 naturally precipitated on the AMO surface in soils while the SM AMO coating was gradually dissolving. When investigating the effect on soil microbiota, AMO efficiently promoted soil microbial activity while no significant changes were observed in the case of Fe III and Fe II,III. The AMO was also able to reduce the uptake of Cd, Pb and Zn by sunflower (Helianthus annuus L.), eliminate Zn phytotoxicity symptoms and increase biomass yield. On the other hand, toxic levels of Mn released from the AMO in an acidic soil were found in sunflower tissues. AMO application is thus recommended for contaminated neutral or slightly alkaline pH with a higher cation exchange capacity in order to avoid unwanted release of Mn. Finally, various types of AMO-biochar composite sorbents were recently prepared and field experiment focused on stabilization of Cd, Pb, Zn and As using studied materials is currently under preparation. The combined results from the thesis highlight the importance of a complex experimental approach dealing with all parts of the contaminated soil environment in order to obtain complete information about the efficiency and usefulness of any newly developed stabilizing amendment.
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Use of Festuca arundinacea for decorative lawns
Doskočil, Jan ; Svobodová, Miluše (advisor) ; Hrevušová, Zuzana (referee)
Use of Festuca arundinacea for decorative lawns
Summary
Festuca arundinacea is briefly bentgrass with broader and coarser leaves. Hardly perennial grass, native to Europe, is well known for its high resistance of dry weather, low intensity of maintenance and resistance of high use. These qualities gains thanks to its well-developed and deep root system, which is capable to gain water and nutrients from deeper parts of soil. Its use is in places with high use, like a race-course, edges of roads or vineyards alleyway. Today, in time of global warming, its usage becomes more important for park purposes and low-input turfs, where is its higher resistance against biotic and abiotic stresses, mainly against drought, utilized. Festuca arundinacea complement well with Poa pratensis in turf.
Goal of this work was to evaluate turfs with Festuca arundinacea and chosen grass species under different mowing frequency. According to hypothesis frequency shouldn´t affect turf coverage. Coverage should be same with different mixture composition with Festuca arundinacea.
The experiment was performed on experimental land of Czech university of Life Sciences Prague, Suchdol in 2015. Mixtures of Festuca arundinacea with Festuca rubra, Poa pratensis and Lolium perenne were seeded together with monocultures of these species in 2012. Mixture composition was 50/50 except mixture of Fesruca arundinacea and Poa pratensis, where the mixture was 75/25. There were conducted 63 plots, in 3 repetitions and in 3 different frequencies of mowing (by 14, 30 and 45 days). Each plot was 6 m2 big. The results were evaluated by analysis of variance ANOVA (P is smaller than 0.05) in program Statgraphics, version XV.
Influence of mixture composition to level of growth was significant. The highest level of growth has monoculture of Festuca arundinacea (10,6 cm). The lowest level of growth has monoculture of Lolium perenne (5,4 cm). Monoculture of Festuca arundinacea had the highest intensity of grow (0,07 cm/day) at 14-day frequency of moving. Lolium perenne has the lowest intensity of grow (0,02 cm/day). At 30-day frequency of mowing mixture of Festuca arundinacea with Poa pratensis has the highest intensity of grow (0,24 cm/day). The lowest intensity of grow has Lolium perenne (0,01 cm/day). The highest intensity of grow was at 45-day mowing frequency. The highest intensity of grow has mixture of Festuca arundinacea with Festuca rubra (0,75 cm/day). The lowest intensity of grow has monoculture of Lolium perenne (0,06 cm/day). Influence of mixture composition to coverage was statistically significant. The highest coverage has mixture of Festuca arundinace with Festuca rubra (81,3 %). The lowest coverage has monoculture of Lolium perenne (58,6%). Influence of frequency to level of growth was statistically significant. The highest level of growth has 45-day frequency of mowing (6 cm) and the lowest level of growth has 14-day frequency of mowing (3,8 cm). Influence of frequency to coverage was statistically significant. The highest coverage 14-day frequency of moving (76,5 %) and the lowest has 45-day frequency of growing (66,7 %).
The knowledge gained will be used for further compilation grass mixtures for park lawns. It turned out that it is better to prefer seeding mixtures with Festuca arundinacea than monocultures. To achieve high coverage and optimal intensity of growth with Festuca arundinacea was recommended to follow 30-day frequency of mowing.
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Assess the current state of nutrition of horses in the specific stables and proposal optimal doses according to the their performance
Burcalová, Helena ; Mudřík, Zdeněk (advisor) ; Václav, Václav (referee)
This work deals with calculations of feed rations of selected thoroughbred horses at the High School of Horse Racing in Prague together with an assessment of economic aspects of horse feeding. The school is mainly focused on the education of jockeys, which means that the work with horses has to conform to the school requirements that need not meet the ideal feeding rhythm of the horses.
United Kingdom norms were compared to the selected Czech norms. Focus was mainly on the racing season, which provides direct comparison of the feed rations with the horses results in the races. The racing season has the highest energetic requirements that need to take into account not only the requirements for the races themselves but also for the resting periods. Feed rations were measured and fed in precise time intervals. Main feeds were oats, hay, bran and Spillers feeds.
During the assessment period a negative side - effect of high temperatures during consecutive heat - wave periods was observed. This aspect may prove important in the future and needs to be taken into account not only for feeding but for the entire horse training.
Out of five examined horses, exceedance of digestible energy requirements was observed with two horses and underestimation with one horse. For two of them the anomaly was in norm. However, the horse with the highest exceedance was experiencing difficulties with feeding, always leaving a part of the ration intact. This made it necessary to adapt the rations to a higher figure than calculated.
Economic aspect of horse feeding needs to be taken into account. The feeding expenses can be decreased by a suitable selection of a feeding mix, however the savings in this regard are not fundamental.
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