The main aim of the diploma thesis is to evaluate the fish management of a trout reserve Svitava 2 and to suggest a correction on the basis of results from the performed surveys and information from the Moravian Fisherman's associotion evidence. Field surveys were realized on 3rd and 4th September 2013. During these surveys 12 fish species out of 5 families were demonstrated by electrofishing. Caught fis were released back to the river measuring weight and lenght. The ichthyologic research was evaulated using indi-cators for fish populations. On account of acquired knowledge and data, I recommend following correction: advance quantity biennial brown trout on 200 fish per hectare, reduce rainbow trout 40 fish per hectare and advence quantity biennial qrayling on 200 fish per hectare.

The Blanice river has its spring in the Šumava Protected Landscape Reserve near Zlatá at an altitude of 972 m a.s.l. and empties in the Otava river near Putim at an altitude of 362 a.s.l. The size of its catchment area is 860,5 km2, the watercourse is 93,3 km and the flow rate at the confluence is 4,23 m3.s-1. The upper reaches of the Blanice has a typical submontane, trout character, which is disturbed by the Husinec reservoir (the water area is 68 ha, maximal depth 25,5 m). The lower two thirds of the river run through an array of ponds in the region of Vodňany and Protivín. This area is intensively cultivated by agricultural activities. These two factors play the major role the fact that the lower part of the river is strongly eutrophicated. This is also supported by the abundance survey, according to which the most abundant species are roach (Rutilus rutilus) and chub (Leuciscus cephalus). The survey was made at 9 localities encompassing the main biotope types in the longitudinal profile of the lower part of the Blanice in the region of Vodňany and Protivín. The harvests were carried out within a 50-meter section, always in the upstream direction towards the place that kept the fish from escape (a small weir, a knickpoint). The most abundant species {--} Rutilus rutilus and Leuciscus cephalus {--} were evaluated from the viewpoint of the age distribution of the population.

Background: Elucidating the role of intestinal drug transporter function in drug development is crucial, as transporter proteins can impact on drug absorption, efficacy and adverse events. In Vitro-In Vivo Extrapolation linked to Physiologically-Based Pharmacokinetic (IVIVE-PBPK) models aim to predict the in vivo impact of transporters from in vitro cell–based transport data and expression-based scaling factors. Currently, these models depend on relative measurements of transporter expression i.e., mRNA or immunoblotting. There is a critical need for physiologically relevant measures of transporter protein abundance to populate these biological frameworks. Objectives: The key objectives were to develop and validate a targeted proteomics workflow to quantify transporter protein abundances in human enterocytes and Caco-2 cells with a QconCAT technique. A cross-laboratory comparison on matched samples was also performed to assess between-laboratory bias in abundance determination. Together with abundance data from each laboratory, BCRP and P-gp transporter activities from Caco-2 cells were used to identify function-abundance relationships, to facilitate the potential development of abundance-function scaling factors. Results: Development of a differential centrifugation technique to obtain plasma membranes was undertaken using MDCK-II and Caco-2 cells. The plasma membrane fraction showed little enrichment from the preceding total membrane fraction and was contaminated with endoplasmic reticulum, as assessed by marker enzyme activities. There were also no differences in Na/K-ATPase, BCRP and P-gp abundances between plasma and total membrane fractions in Caco-2 cells. This may be due to losses of protein from the target membrane fraction, thus, a theoretical framework combining protein assay (BCA) and transporter abundance determinations was proposed. Pilot data on the generation of recovery correction factors using Villin and Na/K-ATPase abundances, to account for protein losses is also presented. The abundances of 6 transporters in jejunal enterocyte membranes (n=3), including the key efflux proteins BCRP (2.56±0.82 fmol/μg), P-gp (1.89±1.07 fmol/μg) and MRP2 (0.59±0.246 fmol/μg) were determined with precision. In addition, peptide losses during protein digestion stages were accounted for in abundance determinations. A cross laboratory comparison of transporter abundances from intestinal (n=4) and Caco-2 cells (n=7) measured in our laboratory and Bertin Pharma (BPh), showed that P-gp abundances were highly correlated (rs=0.72), yet BPh abundances were systematically lower than determined in our laboratory (2.0±2.08 versus. 4.8±3.51 fmol/μg, respectively). No differences or correlations were found for Na/K-ATPase and BCRP abundances between laboratories. A jejunal-Caco-2 cell relative expression factor (REF) for each protein for both laboratories was generated. The P-gp REF was similar for BPh and our laboratory (0.37 vs. 0.4, respectively) however, for BCRP there was a distinct difference (1.11 versus 2.22, respectively). These findings provide the first evidence that employing expression factors generated from abundances quantified in different laboratories may produce altered IVIVE-PBPK outcomes. Functional studies in Caco-2 cells using E-3-S and vinblastine as probes for BCRP and P-gp, respectively, show that protein abundance is more closely correlated to transporter activity than mRNA expression. In addition, it was only possible to verify that increasing P-gp abundances in Caco-2 cells were ranked alongside vinblastine intrinsic clearance, as there was little consistency when estimating Km between the different Caco-2 cell models expressing increasing P-gp abundances, which may be attributed to limited absorptive transport saturation. Thus, forming any conclusions with confidence on concentration dependent abundance-activity relationships was difficult. These data suggest the value of REF scaling factors based on protein abundances, but emphasises the need to generate these from both in vitro and in vivo samples, using the same proteomic workflow. Further work to verify abundance-function relationships is required. Conclusion: A targeted proteomic workflow has been developed allowing quantification of protein abundances for key drug transporters in human gut tissues and cell models. The study has highlighted important areas including losses of targeted proteins, contamination of plasma membrane fractions and standardisation between laboratories that need to be addressed before implementation of transporter abundances into PBPK models is undertaken. Nevertheless, the evidence for a close relationship between transporter abundance and function indicate the potential value of this data for generation of robust REF scaling factors.

The first stars are something many scientists are curious about. How did they formand how did the universe look like at that time? These stars however probably died along time ago, or are at a distance too far away from us to be observable. If these starsexploded and formed supernovae there might be stars observable today that formed fromthe ejecta of these supernovae. Models of nucleosynthesis in the first stars may potentiallybe used to infer parameters of progenitor supernovae from chemical abundances in old,metal-poor stars. This thesis aim is to find out how precise these abundances need to beto achieve a certain precision in the supernova parameters. This is done by perturbingthe abundances for one element at a time in four different stars and see how the recoveredsupernova parameters change. The first conclusion is that it isn’t necessarily the sameelements that are important for determining the supernova parameters in all stars, andif there is one thing that decides which elements are important it would be the star’smetallicity. The stars HE1327-2326 and HE0107-5240 metallicites are close to each other,with [Fe/H] < -5.0 and [Fe/H] = -5.3 respectively, and behaved similarly, the elementmost important in both stars was nitrogen. The star SMSS0313-6708, [Fe/H] < -7.3, hadmore elements that changed the parameters, the most important beeing C, O and Ca.The star CS 31028-001, [Fe/H] = -2.9, also had many elements that were important, andsome of them are Na, K and Ni. / De första stjärnorna är någonting många forskare är nyfikna på. Hur formades deoch hur såg universum ut vid den tiden? Dessa stjärnor dog antagligen länge sedan,eller så är de på ett avstånd för långt bort från oss för att kunna observeras. Om dessastjärnor exploderade och bildade supernovor är det möjligt att det finns stjärnor som gåratt observera som bildades ur dessa supernovor. Modeller av nukleosyntes i dessa förstastjärnor kan potentiellt användas för att anta parametrar för de föregående supernovorur den kemiska sammansättningen för gamla, metalfattiga stjärnor. Målet för dennauppsats är att ta reda på hur exakta värden som behövs på dessa kemiska sammansättningarför att nå en viss säkerhet på supernovaparametrarna. Det görs genom att ändraämneshalten för ett ämne i taget i fyra olika stjärnor och se hur de beräknade supernovamodellsparametrarnaändras. Den första slutsatsen är att det inte nödvändigtvis ärsamma ämnen som är viktiga för att bestämma supernovaparametrarna i varje stjärna,och om det är en sak som bestämmer vilket ämne som är viktigt skulle det vara stjärnansmetallicitet. Stjärnorna HE1327-2326 och HE0107-5240 har metalliciteter som är näravarandra, med respektive [Fe/H] < -5.0 och [Fe/H] = -5.3, och betedde sig snarlikt, så vardet kväve som var det viktigaste ämnet i dessa två stjärnor. Stjärnan SMSS0313-6708,[Fe/H] < -7.3, hade fler ämnen som ändrade parametrarna och de viktigaste var C, O ochCa. Stjärnan CS 31028-001, [Fe/H] = -2.9, hade också många ämnen som var viktiga ochnågra av dem var Na, K och Ni.

The process of in vitro-in vivo extrapolation (IVIVE) can be used to predict pharmacokinetics of drugs in patients using data from in vitro systems. This process relies on the use of experimentally obtained scaling factors, such as abundances of different drug-metabolising enzymes and microsomal protein content (MPPGL). The use of simulators is dependent on abundances and activities of pharmacokinetically relevant enzymes. The incorporation of inter-individual variability in abundances of enzymes, correlations between enzyme expression patterns, and relationships between genetic, physiological, and environmental factors and enzyme expression and activity can make predictions using IVIVE and simulations of pharmacokinetic experiments in virtual populations more accurate and realistic. Incorporation of variability and correlations can also assist in predicting extreme cases where drug therapy may be ineffective or may cause adverse effects. A meta-analysis of 52 studies was carried out to assess the reported abundances of cytochrome P450 and uridine glucuronosyltransferase (UGT) enzymes in adult Caucasian subjects. Some heterogeneity was found between studies and the weighted means and overall coefficients of variation were calculated. Some strong enzyme expression correlations were identified; CYP3A4/CYP3A5*1/*3 (rs = 0.66, p < 0.0001, n = 37), CYP3A4/CYP2C8 (rs = 0.79, p < 0.0001, n = 107), and CYP2C8/CYP2C9 (rs = 0.71, p < 0.0001, n = 72). A quantitative protocol based on targeted proteomics was used to quantify cytochrome P450 and UGT enzymes in adult liver samples (n = 24). The QconCAT standard used for quantification was successfully expressed in-house after optimisation of the expression protocol, and the utility of two strategies in expressing recalcitrant QconCAT proteins was highlighted; the use of a fusion partner and reshuffling the order of peptides in the sequence. The enzymes quantified in this study were CYP1A2, 2A6, 2B6, 2C8, 2C9, 2C18, 2D6, 2J2, 3A4, 3A5, 3A7, 3A43, and 4F2, and UGT1A1, 1A3, 1A4, 1A6, 1A9, 2B4, 2B7, and 2B15. Correlations of expression identified in the meta-analysis were confirmed and new correlations were demonstrated between UGT enzymes and between enzymes from the two families. Correlations between UGT enzymes were particularly strong and statistically significant. Relationships between enzyme expression levels and genotype, age, sex, smoking, and alcohol consumption were investigated. A significant effect of genotype on expression was seen for CYP3A5 (p < 0.0001). An overall moderate decline of expression with age was observed for all the enzymes under study; however, this relationship was not statistically significant in most cases. Gender did not have a considerable effect on expression, although some differences in expression were observed between male and female donors. Smoking seemed to induce the expression of all enzymes; however, statistically significant induction was demonstrated only in the cases of CYP2A6, CYP3A4, CYP3A7, and UGT1A1 (p < 0.05). Alcohol consumption was not shown to have a considerable effect on enzyme expression. Two pig livers were used to optimise some aspects of the experimental protocol including solubilisation and digestion of proteins. Pig MPPGL was measured and relative hepatic contents of drug-metabolising cytochrome P450 enzymes in pig liver were established using label-free quantification.

While we should celebrate the bicentennial of naming the Sumatran rhinoceros (SR), the only extant population on earth might be on the island of Sumatra. Since Strien's 1986 study in Mamas Valley, Leuser, very little more has been learned about how this species distributed and what factors are influencing its extirpation. This study is the first conducted in Sumatra at an Island-wide scale. Using hierarchical models, I estimate the occurrence rates (%) and indices of abundance of SR on three remaining population areas: Leuser Landscape (LL) in 2007 (2.77%, 26 (CI 12-61)), Way Kambas (WK) in 2008 (33.58%, 27 (CI 14-50)) and Bukit Barisan Selatan (BBS) in 2010 (36.4%, 31 (CI 19-66)). Primary dry land forest and rivers are factors affecting SR occurrence in LL, but the index of abundance also is affected by deforestation, roughness of terrain, and and a vegetation index. The index of abundance in WK is more affected by major roads, and brush and savannah cover types, and the occurrence there is additionally affected by deforestation. Secondary dry land forest, regular roads, and deforestation is affecting both the occurrence rate and index of abundance of SR in BBS. The identification of these environmental and disturbance factors is translated into spatially explicit map that can be used to update the IUCN distribution map. In LL, by comparison to the historical distribution based on Strien (1986), the small population in Bendahara Mountain might still persist outside the core population in Mamas Valley.

Up to 87% of the world’s wetlands have been destroyed, considerably reducing ecosystem services these wetlands once provided. More recently, many wetlands are being restored in an attempt to regain their ecosystem service. This study seeks to determine the effects of restored wetlands on local bat habitat use. Bat activity was found to be significantly higher around the wetlands when compared to distant grassy fields; however, no significant difference was found among the restored wetlands and a remote cattle farm containing multiple water features. Geospatial models of bat distribution and bat foraging were produced using machine learning that showed higher habitat suitability and foraging activity around restored wetlands than around distant grassy fields, suggesting that wetlands provide vital habitat for insectivorous bats. This study demonstrates that restored wetlands promote bat activity and bat foraging, and restoring wetlands may be a useful means of increasing natural pest control over nearby farmlands.

Impatiens glandulifera is an invasive species throughout Europe. It was introduced to the wild in 1918 by escape from private gardens as well as the transport of garden soil and waste. Impatiens glandulifera prefers moist soils with moderate shade and commonly grows in riparian environments. In the Umeå municipality in northern Sweden, where this study is focused, the number of Himalayan balsam observations has dramatically increased over the last few years. This study aimed to determine habitat and anthropogenic land-use factors that may have contributed to the spread of Himalayan balsam in the Umeå municipality. This was done by using data on recorded observations of the species in a database called Artportalen. In order to determine how abundant and in which habitats Himalayan balsam occurs in the Umeå municipality, data on recorded observations in Artportalen from the Umeå municipality region for the period 01-01-2021 to 31-12-2021 was used along with maps from Google Earth Pro and Google maps. It was found that Himalayan balsam is now common in the region and does not show a definitive preference for riparian habitats or for forest or open areas in the Umeå municipality. Human activities seemed to be the main contributor to the spread of Himalayan balsam in the Umeå municipality.

<p>Little is known about how the leaf bacterial community is affected by the seed microbiota at different stages of plant development. The bacterial populations of spinach seed and leaves after germination were compared using DGGE, to assess bacterial community richness, and real-time PCR to compare the abundance of select phyla (total bacteria, <i>Actinobacteria, Bacteroidetes, Firmicutes, α-Proteobacteria and β- Proteobacteria</i>). To determine the effect of environment, the plants were grown in the field and growth chambers. Vertical transmission of bacterial community members was evident; the developmental stage of the plant affected the richness and abundance of select bacterial phyla. The bacterial richness of plants grown in the two environments was not affected. However, overall numbers of bacteria increased in field grown samples in comparison to those produced in growth chambers during development. A statistically significant interaction was seen between growth stage and environment with each of the selected phyla. Populations on cotyledons were smaller than mature leaves, but were not significantly different than the 3-4 leaf stage plants. The culturable populations of bacteria on seeds (~5 log CFU/g) were significantly smaller than determined using real time PCR (~7 log copies). Of these bacteria cultured from spinach seeds, isolates belonging to the genera <i>Pantoea</i> were found to inhibit growth of <i>E. coli</i> O157:H7 <i>in vitro</i>. This study highlights the importance of vertical transmission on the bacterial community of plants and suggests the importance of developing strategies to influence these communities on seed to control human and plant pathogens on the leaf surface.</p> / Master of Science

Growing concerns over the possible effects of greenhouse-gas-related global warming on North American forests have led to increasing calls to address climate change effects on forest vegetation in management and planning applications.  The objectives of this project are to model contemporary conditions of soils and climate associated with the presence or absence and abundance of five southern pine species: shortleaf pine (Pinus echinata Mill.), slash pine (P. elliottii Engelm.), longleaf pine (P. palustris Mill.), pond pine (P. serótina Michx.), and loblolly pine (P. taeda L.).  Classification and regression based Random Forest models were developed for presence-absence and abundance data, respectively.  Model and diagnostics such as receiver operating curves (ROC) and variable importance plots were examined to assess model performance.  Presence-absence classification models had out-of-bag error rates ranging from 6.32% to 16.06%, and areas under ROC curves ranging from 0.92-0.98.  Regression models explained between 13.76% and 43.31% of variation in abundance values.  Using the models based on contemporary data, predictions were made for the future years 2030, 2060, and 2090 using four different greenhouse gas emissions scenarios and three different general circulation models.  Maps of future climate scenarios showed a range of potential changes in the geographic extent of the conditions consistent with current presence observations.  Results of this work will be incorporated into eastern U.S. variants of the Forest Vegetation Simulator (FVS) model, similar to work that has been done for FVS variants in the West. / Master of Science