Radiotherapy is often used to treat prostate cancer. While using high dose of radiation does kill cancer cells, it can cause toxicity in healthy tissues for some patients. It would be best to apply this treatment only to patients who are likely to be immune from such toxicity. This requires a classifier that can predict, before treatment, which patients are likely to exhibit severe toxicity. Here, we explore ways to use certain genetic features, called Single Nucleotide Polymorphisms (SNPs), for this task. This thesis uses several machine learning methods for learning such classifiers for predicting toxicity. This problem is challenging as there are a large number of features (164,273 SNPs) but only 82 samples. We explore an ensemble classification method for this problem, called Mixture Using Variance (MUV), which first learns several different base probabilistic classifiers, then for each query combines the responses of the different base classifiers based on their respective variances. The original MUV learns the individual classifiers using bootstrap sampling of the training data; we modify this by considering different subsets of the features for each classifier. We derive a new combination rule for base classifiers in the proposed setting and obtain some new theoretical results. Based on characteristics of our task, we propose an approach that involves first clustering the features before selecting only a subset of features from each cluster for each base classifier. Unfortunately, we were unable to predict radiation toxicity in prostate cancer patients using just the SNP values. However, our further experimental results reveal strong relation between correctness of a classifier in its prediction and the variance of the response to the corresponding classification query, which show that the main idea is promising.

Acid soils limit the growth of aluminum-(Al) sensitive crops such as alfalfa (Medicago sativa L.). Management of acid subsoils can be difficult due to physical and economic constraints. Field experiments were conducted at two locations to evaluate the effectiveness of surface-applied gypsum and a flue gas desulfurization by-product for reducing the toxic effects of acid subsoils on alfalfa. The materials were applied at rates of 0, 5, 10, and 15 Mg ha-1. In addition, a glasshouse experiment was conducted that used 0, 5, and 10 Mg ha-1 of gypsum only. Field studies were concluded 41 and 45 months after treatment application at the two locations. No effect of material on alfalfa yield or tissue mineral concentration was observed. Also, rate did not affect yield. However, there were differences in plant tissue mineral concentration in several harvests that were related to rate. Soil was sampled periodically to 120 cm and indicated movement of Ca and S into the soil profile to depths of 60 and 120 cm, respectively. Subsoil pHH2O and pHCaCl2 were not affected by treatment. Extractable and exchangeable Al were not reduced by movement of Ca and S into the soil. In the glasshouse study, alfalfa yields and root growth were not affected by gypsum rate. As gypsum rate increased, plant tissue S increased, but K and Mg decreased. Alfalfa roots did not grow below 60 cm, even though there was indication of material movement to 90 cm in the soil. Although sulfur moved to 75 cm, no effect on soil Al was observed. Leachate collected from the bottoms of columns indicated that soil cations were leached as a result of gypsum application. Gypsum and the flue gas desulfurization by-product did not significantly affect the acid soils used in these studies or improve alfalfa growth.

Epidemiological evidence suggest that exposure to endocrine disrupting compounds (EDCs) is a risk factor for diseases that involves the cardiovascular system but we know little about the mechanisms whereby these compounds can cause injury in the vasculature. The aim of this thesis was to characterize the effects and mechanisms of some EDCs in vascular cells and highly vascularized tissues. Elevated exposure to environmental EDCs is associated with an increased risk for cardiovascular diseases. In vitro studies demonstrated that the environmental EDCs, 1-nitropyrene, PCB126 and bisphenol A, caused distinct changes in primary human endothelial cells. 1‑Nitropyrene induced cell stress and DNA damage, PCB126 caused changes that indicate endothelial dysfunction and vasoconstriction, and BPA induced changes that indicate angiogenesis and vasoconstriction. Further studies demonstrated that long-term exposure of rats to BPA induced changes in rat cardiac tissues in vivo similar to those observed in human endothelial cells in vitro. The type of cellular alterations that were demonstrated is known to play to play a role in cardiovascular disease in humans. These findings suggest that environmental EDCs can cause damage to the human endothelium that may contribute to the development of cardiovascular disease. The beneficial effects of the pharmaceutical EDC tamoxifen in breast cancer treatment are compromised by an increased risk for bleedings, hyperplasia, and cancer in the endometrium. Ex vivo studies identified the glandular and surface epithelia as potential target sites for tamoxifen adduct formation and tamoxifen-induced cell stress the human endometrium. No signs of tamoxifen-induced changes were detected in the blood vessels. The results suggest that bioactivation of tamoxifen and subsequent cell injury in endometrial epithelial cells may play a role for tamoxifen’s side effects in the endometrium. Taken together, this thesis provide evidence that may help understanding how exposure to EDCs can increase the risk for diseases in that involves the cardiovascular system.

Aluminium (Al) has been recognised as a main toxic factor alongside pH in acidified water ecosystems. The toxic effect of Al has been attributed to inorganic Al (Ali), though there are few in situ studies in ambient humic waters which are the focus of this thesis. The aim was to estimate Ali toxicity and thus also Ali concentrations in Swedish humic streams. Subsequently it is necessary to analyse Ali correctly, which was studied by modelling and method intercalibrations. The hypothesis was that the effect of Ali could be followed via physiological effects and Al accumulation, as well as by mortality. Toxicity was studied by in stream exposures of brown trout (Salmo trutta L.) and two salmonid prey organisms (Gammarus pulex and Baetis rhodani) during spring flood. The modelling of the Ali fraction was performed using monitoring data covering all of Sweden with satisfactory results. The essential variables for Ali modelling were determined; Al, DOC, pH and F, while Fe, Ca and Mg had less effect. The automated analytical procedure for Ali (with cation exchange followed by complexation with pyrocatechol violet) was modified and validated and showed to be the preferred method for laboratory analyses. To avoid detrimental effects for brown trout Ali should be <20 µg/L and pH >5.0; mortality was high when the Ali was above 50 µg/L. The invertebrates were more sensitive, as mortalities occurred at pH <6.0 and Ali >15 µg/L for G. pulex, and at pH <5.7 and Ali >20 µg/L for B. rhodani. It is prudent to use a wide view and let the most sensitive species set the tolerance limits; a pH above 5.7-6.0 and Ali below 15-20 µg/L allows the stream ecosystems to thrive. Today, as waters are recovering from acidification, the aim of mitigating liming is to carefully adjust dosage to avoid suboptimal water quality. The thresholds found in this thesis can be used to efficiently but carefully decrease liming, as both Ali and pH levels have to be balanced to sustain the recovering aquatic biota.

High chronic fructose consumption is linked to a nonalcoholic steatohepatitis (NASH) type of hepatotoxicity. Oxalate is the major endpoint of fructose metabolism, which accumulates in the kidney causing renal stone disease. Both diseases are life-threatening if not treated. Our objective was to study the molecular cytotoxicity mechanisms of fructose and some of its metabolites in the liver. Fructose metabolites were incubated with primary rat hepatocytes, but cytotoxicity only occurred if the hepatocytes were exposed to non-toxic amounts of hydrogen peroxide such as those released by activated immune cells. Glyoxal was most likely the endogenous toxin responsible for fructose induced toxicity formed via autoxidation of the fructose metabolite glycolaldehyde catalyzed by superoxide radicals, or oxidation by Fenton’s hydroxyl radicals. As for hyperoxaluria, glyoxylate was more cytotoxic than oxalate presumably because of the formation of condensation product oxalomalate causing mitochondrial toxicity and oxidative stress. Oxalate toxicity likely involved pro-oxidant iron complex formation.

Vigabatrin (VGB) is an anti-epileptic drug used to treat children with Infantile Spasms (IS). The 3.0 flicker amplitude of the electroretinogram (ERG) is currently used to monitor visual function changes in infants on VGB. To find a more specific marker of permanent changes due to VGB, sedated ERGs were performed on 31 IS patients and 13 retinally normal controls to isolate components of the cone pathway. ERG growth curves, for each component, recorded from children with IS were generated using data recorded pre-VGB treatment and for controls. Only the cone off response (from Off bipolar cells) and cone photoreceptor sensitivity were associated with decreased flicker amplitude. Twenty nine percent of patients had an abnormal cone off response. No patient had an abnormal cone off response at baseline. No patient with an abnormal cone off response recovered normal function. The cone off response could serve as a marker VGB retinal toxicity.

High chronic fructose consumption is linked to a nonalcoholic steatohepatitis (NASH) type of hepatotoxicity. Oxalate is the major endpoint of fructose metabolism, which accumulates in the kidney causing renal stone disease. Both diseases are life-threatening if not treated. Our objective was to study the molecular cytotoxicity mechanisms of fructose and some of its metabolites in the liver. Fructose metabolites were incubated with primary rat hepatocytes, but cytotoxicity only occurred if the hepatocytes were exposed to non-toxic amounts of hydrogen peroxide such as those released by activated immune cells. Glyoxal was most likely the endogenous toxin responsible for fructose induced toxicity formed via autoxidation of the fructose metabolite glycolaldehyde catalyzed by superoxide radicals, or oxidation by Fenton’s hydroxyl radicals. As for hyperoxaluria, glyoxylate was more cytotoxic than oxalate presumably because of the formation of condensation product oxalomalate causing mitochondrial toxicity and oxidative stress. Oxalate toxicity likely involved pro-oxidant iron complex formation.

Vigabatrin (VGB) is an anti-epileptic drug used to treat children with Infantile Spasms (IS). The 3.0 flicker amplitude of the electroretinogram (ERG) is currently used to monitor visual function changes in infants on VGB. To find a more specific marker of permanent changes due to VGB, sedated ERGs were performed on 31 IS patients and 13 retinally normal controls to isolate components of the cone pathway. ERG growth curves, for each component, recorded from children with IS were generated using data recorded pre-VGB treatment and for controls. Only the cone off response (from Off bipolar cells) and cone photoreceptor sensitivity were associated with decreased flicker amplitude. Twenty nine percent of patients had an abnormal cone off response. No patient had an abnormal cone off response at baseline. No patient with an abnormal cone off response recovered normal function. The cone off response could serve as a marker VGB retinal toxicity.

Essential metals like Ca2+ and Zn2+ play critical roles in biological processes through protein interactions. Conversely, non-essential metals (e.g., Gd3+ and Pb2+) also interact with proteins, often with toxic effects. Molecular metal toxicity is assumed to be due to ionic displacement, and studies have demonstrated that Pb2+ replaces Zn2+, Ca2+ and other essential metals in proteins. The focus of this work was to compare protein Ca2+ and Pb2+ -binding sites and to investigate a mechanism of Pb2+ toxicity in Ca2+-binding proteins, particularly the intracellular trigger protein calmodulin (CaM) which binds four Ca2+ ions and interacts with numerous molecular targets via Ca2+-induced conformational change. A statistical analysis of PDB structural data for Pb2+ and Ca2+-binding (EF-hand and non-EF-hand) proteins revealed fewer binding ligands in Pb2+ sites (4 ± 2), than non-EF-Hand (6 ± 2) and EF-Hand (7 ± 1) Ca2+-binding sites. Pb2+ binds predominantly with sidechain Glu (38.4%), which is less prevalent in both non-EF-Hand (10.4%) and EF-Hand (26.6%) sites. Interestingly, analyses of proteins where Pb2+ replaces Ca2+ (calmodulin) or Zn2+ (5-aminolaevulinic acid dehydratase) revealed structural changes presumably unrelated to ionic displacement. These results suggested that Pb2+ adopts diverse binding geometries and that opportunistic binding outside of known Ca2+-binding sites may play a role in molecular metal toxicity. Ca2+-binding affinities (Kd) using phenylalanine and tyrosine fluorescence were found to be 1.15 ± 0.68 X 10-5 M and 2.04 ± 0.02 X 10-6 M for the N- and C-terminal domains, respectively. The Kd for Pb2+-binding in the N-terminal domain, 1.40 ± 0.30 X 10-6 M, was 8-fold higher than Ca2+. Binding of Pb2+ in the C-terminal domain produced a biphasic response with Kd values 7.34 ± 0.95 X 10-7 M and 1.93 ± 0.32 X 10-6 M, suggesting a single higher affinity Pb2+-binding site in the C-terminal domain with nearly equivalent affinity for the remaining sites. Competitive effects of Pb2+ added to Ca2+-loaded CaM were examined using multiple NMR techniques. Pb2+ was found to displace Ca2+ only in the N-terminal domain, however structural/dynamic changes were observed in the central helix apparently due to Pb2+-binding in secondary sites. These data supported our hypothesis that CaM structure and function is altered by opportunistic Pb2+-binding.

Previous studies exposing fish to xenoestrogens have demonstrated vitellogenin (VTG) induction, delayed gametogenesis, altered sex distribution, and decreased reproductive performance, with a majority of those studies focusing on exposure to single chemicals. The objective of this study was to determine the effects of binary mixtures of a weak estrogen receptor agonist, nonylphenol (NP) and a potent estrogen receptor agonist, 17α-ethinylestradiol (EE) on sex distribution, gametogenesis, VTG induction, heat shock protein 70 (HSP70) expression and reproductive capacity in zebrafish (Danio rerio). Fish were exposed from 2 to 60 days post-hatch (dph) to nominal concentrations of 10 or 100 µg/l NP (NP10 or NP100, respectively), 1 or 10 ng/l EE (EE1 or EE10, respectively), 1 ng/l EE + 10 or 100 µg/l NP (EE1+NP10 or EE1+NP100, respectively), 10 ng/l EE + 10 or 100 µg/l NP (EE10+NP10 or EE10+NP100, respectively) or solvent control (0.01% acetone v/v) in a static-renewal system with replacement every 48h. At 60 dph, fish from each treatment were euthanized for histological examination of gonads, and whole body VTG and HSP70 levels. Remaining fish were reared in clean water until adulthood (240 dph) for breeding studies. In all EE10 exposure groups (EE10, EE10+NP10 and EE10+NP100), increasing NP concentration acted less than additively to the action of EE in terms of VTG induction at 60 dph. Similarly, a less than additivity of effect was observed with egg production, where EE1+NP100 exposure resulted in significantly more eggs produced per breeding trial than EE1 alone. Histological staging of oogenesis revealed suppressed gametogenesis in females at 60 dph. There were no differences among treatment groups in whole body HSP70 expression in 60 dph fish or in gonadal HSP70 expression in adult fish. Although there was no statistical evidence of non-additivity, breeding trials in adults revealed significant reductions in egg viability, egg hatchability and/or F1 swim-up success, suggesting that developmental exposures to xenoestrogens may cause irreversible effects on egg quality and progeny even after depuration. In conclusion, these results suggest that environmentally relevant mixtures of NP and EE can produce additive or non-additive effects depending on the particular response being determined and the respective exposure concentrations of each chemical. Thus, it is recommended that caution be exercised in ecological risk assessments when assuming additivity in piscine responses to xenoestrogen mixtures.