The biochemical pathway for the anaerobic degradation of gallate, pyrogallol and phloroglucinol by Eubacterium oxidoreducens was investigated. Phloroglucinol reductase was purified 90-fold, from the soluble fraction of cell extract, to electrophoretic homogeneity. The enzyme was an α₂ homodimer with a native M_r of 78,000, did not contain metals or cofactors and was specific for phloroglucinol and NADPH with a K_m of 800 μM and 6.7 μM respectively at pH 6.8. The Km for phloroglucinol decreased with increasing pH. The enzyme catalyzed reaction was reversible and the equilibrium constant was 9.6. Dihydroresorcinol was a competitive inhibitor of the reverse reaction (K_i = 756 μM). Dihydrophloroglucinol produced in cell extract with H₂ as the reductant was identical to the compound produced by sodium borohydride reduction of phloroglucinol as shown by ¹H NMR spectroscopy. The ¹³C NMR spectrum was consistent with the structural assignment of dihydrophloroglucinol. The mechanism of the proposed enzymatically catalyzed reaction is proposed to involve transfer of a hydride equivalent from NADPH to the carbonyl carbon of the phloroglucinol dianion. Mutant strains of E. oxidoreducens that showed no gallate decarboxylase or dihydrophloroglucinol hydrolase activity were isolated after mutagenesis with ethylmethane sulfonate and emichment with ampicillin. The decarboxylase deficient mutants were unable to grow on gallate while pyrogallol and phloroglucinol supported growth. The hydrolase deficient mutants were unable to grow on any aromatic substrates and converted gallate to pyrogallol and dihydrophloroglucinol. The conversion of gallate to non-aromatic intermediates by cell extract of the wild-type stain was dependent on the presence of 1,2,3,5-benzenetetrol for the conversion of pyrogallol to phloroglucinol and on formate for the reduction of phloroglucinol to dihydrophloroglucinol. Transhydroxylase activity involved in the conversion of pyrogallol to phloroglucinol was induced by growth on aromatic substrates. The formate dehydrogenase was located in the soluble fraction of cell extract, and activity was protected from oxygen inactivation by sodium azide. The Km for formate and NADP was 290 μM and 140 μM respectively at pH 7.5. The pH optimum for activity was 7.5 and maximum activity was observed at a temperature of 50°C. / Ph. D.

A groundwater monitoring study was conducted as part of a comprehensive program to remediate a former wood-preserving site that was contaminated with creosote. Twenty-five multi-level samplers (MLSs) were installed on-site and groundwater samples were collected and tested regularly between March 1998 and July 2000. Nearly one-thousand hybrid poplar trees were planted on-site in 1997 to help contain the groundwater plume and enhance phytoremediation. Ten polycyclic aromatic hydrocarbons (PAHs) were monitored along with several terminal electron acceptors (TEAs) and their reduced end products. The focus of the study was to determine the extent of natural biodegradation in the subsurface and assess the role of the poplar trees in site remediation. Since monitoring began, considerable progress has been made remediating the site and the contaminant plume has been shrinking consistently. PAH levels in the groundwater and soil have been reduced and individual MLSs show consistently decreasing contamination. At this point in the study it cannot be conclusively determined what impact the poplar trees are having on the progressing site remediation. However, there is a wealth of evidence indicating that natural biodegradation is playing a major role in site cleanup. Monitoring of TEAs indicates suggests that there are aerobic zones in the site aquifer, but that reduced conditions exist as well. Dissolved oxygen (DO) was found in many MLS ports, but other ports were devoid of both DO and nitrate and contained large quantities of aqueous Fe(II). Oxygen, nitrate and Fe(III) are being reduced on-site and data suggests that they are being used in the biological oxidation of PAHs. Although laboratory studies document the oxidation of PAHs under sulfate-reducing conditions, high aqueous sulfate values were recorded throughout the site, regardless of the level of contamination. Several possible mechanisms are proposed to explain the coexistence of high sulfate and PAHs in the site aquifer. The system may be redox-buffered by excess solid Fe(III) and Mn(III, IV) oxides. Also, dissimilatory sulfate-reducers are strict anaerobes and oxygen-rich rainwater may be toxic to them. The presence of a layer of coal below land surface creates pyrite oxidation conditions similar to those encountered in conjunction with acid mine drainage. The MLSs most affected by the coal layer have less PAHs and DO, lower pH, and higher sulfate and Fe(II) levels than other wells. The oxidation-reduction status of each MLS, based on oxygen, nitrate and Fe(II) measurements, appears to be closely related to the level of PAH contamination, suggesting that PAHs are the primary substrate being biologically oxidized in the site aquifer. These findings tend to support the general belief that the major limitation to natural biodegradation in subsurface environments is the delivery of adequate supplies of suitable TEAs to contaminated zones. / Master of Science

Amino polyaromatic hydrocarbons (amino PAHs) and nitro polyaromatic hydrocarbons (nitro PAHs), two highly mutagenic classes of compounds, are proposed to be metabolized to an electrophilic aryl nitrenium ion which attacks DNA and forms DNA adducts. A structure-activity relationship was investigated between aryl nitrenium ion stability and mutagenic activity. Arylnitrenium stability for seventeen amino PAHs was measured using electron ionization mass spectrometry. The ratio of [M-1]⁺/M⁺ intensities was used as an indicator of nitrenium ion stability. These values were then compared to mutagenicity data from the Ames Salmonella assay. Physical descriptors of isomer classification (based on ring size and shape) and isomer position of substitution were used in the statistical analysis. A strong correlation between mutagenicity, isomer classification, and stability was found (r²= 0.899 and p<0.001). This finding agrees with reported literature that the compound's physical features of ring size and position of substitution affect mutagenicity. A high correlation of r² = 0.955 was found between mutagenicity, isomer classification, and stability for three sets of isomers: 1- and 2-aminoanthracene, 1- and 2-aminonaphthalene, and 1- and 2-aminofluorene. The nitrenium ion formed from the 2 position was found to be less stable and more mutagenic than the 1 position. This finding agrees with correlations found between mutagenicity and LUMO (Lowest Unoccupied Molecular Orbital) calculations of the electrophilicity of the nitrenium ion. These results indicate that the less stable the nitrenium ion within an isomer pair, the more mutagenic the amino PAH. / Master of Science

Thesis (M.Tech.: Biotechnology)-Dept. of Biotechnology, Durban University of Technology, 2007 xv, 136 leaves / The chemical and biological properties of the essential oil from Cymbopogon validus were investigated. Hydro-distillation was used to extract the oil from C. validus, the flower-heads, leaves, culms and rhizomes. The percentage oil yields obtained from the plant organs varied from 0.05 to 1.23%, with the greatest concentration found in the flower-heads and rhizomes, 1.23 and 1.12% respectively. A sensory evaluation of the oil revealed that the essential oil was slightly murky, pale yellow in colour, had a strong turpentine-like smell and remained liquid at room temperature. The oxidative stability of C. validus oil was evaluated by determining its Rancimat induction period (negative), peroxide value (60.56 meq/kg), iodine value (84.55), percentage free fatty acids (0.19%) and percentage cholesterol (3.03%). These results indicated that the oil was highly susceptible to oxidation. Chromatographic profiles of the oils from C. validus, as well as the plant organs were generated using gas chromatography-mass spectroscopy (GC-MS). Predominant compounds present in the oil included alpha-Cubebene, Camphene, Geraniol, Limonene, Myrcene, Palmitic acid and Sabinene. C. validus essential oil was also investigated for its antimicrobial (disk diffusion), antioxidant (1, 1-Diphenyl-1-Picrylhydrazyl (DPPH) assay), anti-inflammatory (5-lipoxygenase assay), anti-mosquito properties (insecticidal, larvicidal and repellency assays) and toxicity profile (Brine shrimp and Ames assays). The oil showed poor antimicrobial activity and inhibited the growth of only Gram positive bacteria with a minimum inhibitory concentration (MIC) of 0.0625 (vol/vol) for Bacillus, Micrococcus and Staphylococcus species. The oil also exhibited excellent antioxidant activity, scavenging more than 80% of DPPH free radicals and possesses anti-inflammatory activity (IC50=190 ppm). C. validus oil showed good adulticidal activity (53.7% mortality) and excellent larvicidal (100% mortality) and repellent activity (100% repellency) against Anopheles arabiensis mosquitoes. At high concentrations, the oil was toxic to brine shrimp larvae. However, when diluted it was safe and the minimum inhibitory concentration was 0.0001(vol/vol). The absence of revertant colonies at all essential oil concentrations in the Ames test suggest that the oil is not mutagenic. These results lead the way for exploiting C. validus oil as a multi-functional agent that has antibacterial, anti-oxidant, anti-inflammatory, and anti-mosquito properties.

Experimental mole fraction solubilities of benzil, thianthrene, trans-stilbene, thioxanthen-9-one, diphenyl sulfone and dibenzothiophene sulfone are determined in pure noncomplexing and complexing solvents. Predicted solubility values are calculated for benzil, thianthrene, trans-stilbene and thioxanthen-9-one using expressions derived from Mobile Order theory. Large deviations between experimental and predicted solubilities in alcohol solvents exist, therefore optimized solute - solvent association constants are determined. Previously measured thianthrene solubilities in five binary alkane + cyclohexane solvent mixtures are compared with values predicted from Mobile Order theory using the measured solubility in each of the pure solvents as input parameters. The experimental mole fraction solubility of benzil in eight binary alcohol + 1-octanol solvent mixtures are also measured and compared with predicted values.

Thesis (M.Sc. (Chemistry)) --University of Limpopo, 2017 / The presence of polycyclic aromatic hydrocarbons (PAHs) in the environment is of major concern since these compounds are highly persistent, toxic and wide spread pollutants. The aim of this study was to evaluate the levels of PAHs in water and sediment samples collected from Blood and Mokolo Rivers in Limpopo Province, South Africa. Liquid-liquid extraction (LLE) was used for the extraction of PAHs from water, whereas PAHs in sediments were extracted using optimised microwaveassisted extraction (MAE). Furthermore, ultrasonication and a combination of ultrasonication and mechanical agitation were used for the extraction of PAHs from sediments samples. The quantification of sixteen (16) PAHs in water and sediment was carried out using gas chromatography-mass spectrometry (GC-MS) in selected ion monitoring (SIM) mode and by GC-flame ionisation detector (GC-FID). Concentrations of PAHs in sediments were higher than in water. The highest concentrations of PAHs were obtained in Mokolo River sediments, with the concentration ranging between 0.044 and 51.9 mg/kg. The levels of PAHs recorded in Blood River sediments were lower than those obtained in Mokolo River with concentrations ranging between 0.014 and 3.10 mg/kg. In water samples, higher levels of PAHs were observed in Mokolo River (between 0.0219 and 1.53 µg/L) while lower concentrations were recorded in Blood River (between 0.0121 and 0.433 µg/L). In water and sediment samples from both Rivers, higher molecular weight (HMW) PAH compounds (4-6 rings) were found at greater concentration levels than lower molecular weight (LMW) PAHs (2-3 rings), and this can be attributed to pyrogenic activities in the study areas. The efficiencies and accuracy of the methods for the extraction of PAHs were determined by assessing the recoveries of samples spiked with known amount of standards (for water samples), while a certified reference material (CRM) was used for sediments. Percentage recoveries ranged from 67.6 to 115% for LLE and 83.8 to 125% for MAE for both sample types. Diagnostic ratio was used for the source identification of PAHs in sediment samples. Several PAHs ratios indicated that both pyrogenic and petrogenic could be the sources of these compounds in both rivers. Toxic equivalency factors (TEFs) and benzo(a)pyrene equivalent (BaPE) were used to quantitatively estimate the PAHs potential human health risk. The assessment of ecotoxicological risk indicated that the v sediment samples collected from Mokolo River are at high toxicity risk while sediments from Blood River are at low sediment toxicity risk. / Water Research Commission (WRC), National Research Foundation (NRF) and Sasol Inzalo Foundation

During the past 30 years, numerous studies have focused on the toxicities of polycyclic aromatic hydrocarbons (PAH). Laboratory and field studies have helped elucidate the detrimental effects of these chemicals on growth, reproduction and immune response. Polycyclic aromatic hydrocarbons are in the priority list of chemicals to be studied by different governmental agencies and universities and understanding their mechanisms of action is the focus of the current research. The manuscripts presented in this dissertation are focused on the effects and mechanism of action of PAH on disease susceptibility. After a dietary exposure to PAH for up to 50 days (chapter II) and samplings after 3, 7, 14, 28 and 50 days, a number of biomarkers of PAH exposure were measured: Fluorescent aromatic compounds (FACs) in bile, ethoxyresorufin-o-deethylase (EROD) in liver microsomes, cytochrome P450 1A immunohistochemistry in liver and kidney and adduct formation in liver. Additionally markers of oxidative stress were measured: comet assay in blood, protein nitration in kidney and F2-isoprostanes in kidney. Oxidative stress was a probable factor in PAH induced responses in fish adapted to long-term PAH exposures and aryl hydrocarbon activation was not necessarily involved in this process. Disease challenge with Aeromonas salmonicida (chapter III) resulted in differences in mortalities that demonstrated that fish exposed to PAH were more susceptible to disease than fish not exposed to PAH. Determination of gene expression in head kidney of fish exposed and not exposed to PAH challenged with A. salmonicida using microarray and RT-PCR technologies 2, 4, 10 and 20 days after challenge (chapter IV), suggested that PAH exposure was associated with down regulation of interleukin 8, transport associated protein 1, NF-kB modulator, recombination activating gene and major histocompatibility complex II two days after challenge in fish exposed to PAH. The transcript levels were closer to control levels 20 days after challenge, this indicated a recovery from the effect of PAH exposure. / Graduation date: 2006

Thesis (M.Sc.)--Memorial University of Newfoundland, 2005. / Restricted until October 2006. Bibliography: leaves 99-106.

Alkyl-polycyclic aromatic hydrocarbons (alkyl-PAHs) constitute more than 90% of the total PAHs in crude oil and are the main constituents toxic to fish. Little characterization of alkyl-PAHs has been reported and is needed to predict the effects of crude oil following spills. The objectives of this thesis were: (1) to evaluate the toxicity of alkyl-phenanthrenes and alkyl-anthracenes to the early life-stages of medaka (Oryzias latipes) using the partition controlled delivery of toxicants (PCD); (2) to investigate the effect of light on alkyl-anthracene toxicity; (3) to further characterize the PCD method; (4) to better understand alkyl-PAH mechanisms of toxicity; and (5) to identify the major phase I and phase II alkyl-PAH metabolites in rainbow trout (Oncorhynchus mykiss) and in medaka by both in vitro and in vivo methods. It was determined that the toxicity of both series of alkyl-PAHs increased with the number of carbon substituents on the rings. Some alkyl-PAHs had EC50 values lower than the value from conventional semi-static exposure methods. These values were below the water solubility limit, consistent with the ability of PCD to correct for values from nominal concentrations above solubility. PCD provided stable concentrations for up to 17 days but could not always compensate for losses of alkyl-anthracenes by photodegradation. Both series of alkyl-PAHs were toxic through different mechanisms that resulted from their physical and chemical properties. Alkyl-phenanthrenes such as 7-isopropyl-1-methylphenanthrene (retene) were more toxic to medaka embryos than phenanthrene. The appearance of blue sac disease suggested toxicity enhancement through the aryl hydrocarbon receptor pathway. Alkyl-anthracenes were toxic by narcosis in the absence of light and by phototoxicity in the presence of light. The photoproducts of alkyl-anthracenes were not toxic to fish. The in vitro phase I metabolism by rainbow trout CYP1a enzymes and in vivo phase II metabolism in rainbow trout produced alkyl-anthracenes metabolites substituted mainly on the ring system. The phase II in vivo metabolites of alkyl-phenanthrenes in medaka larvae were substituted mainly on their alkyl chains. For all alkyl-PAHs, a predominance of glucuronide conjugates was identified in the phase II metabolites. This characterization of the toxicity of alkyl-PAHs may contribute to predicting the toxicity of crude oil based on its composition. / Thesis (Ph.D, Chemistry) -- Queen's University, 2008-08-29 14:18:10.308

Thesis (M.Tech.: Biotechnology)-Dept. of Biotechnology, Durban University of Technology, 2007 xv, 136 leaves / The chemical and biological properties of the essential oil from Cymbopogon validus were investigated. Hydro-distillation was used to extract the oil from C. validus, the flower-heads, leaves, culms and rhizomes. The percentage oil yields obtained from the plant organs varied from 0.05 to 1.23%, with the greatest concentration found in the flower-heads and rhizomes, 1.23 and 1.12% respectively. A sensory evaluation of the oil revealed that the essential oil was slightly murky, pale yellow in colour, had a strong turpentine-like smell and remained liquid at room temperature. The oxidative stability of C. validus oil was evaluated by determining its Rancimat induction period (negative), peroxide value (60.56 meq/kg), iodine value (84.55), percentage free fatty acids (0.19%) and percentage cholesterol (3.03%). These results indicated that the oil was highly susceptible to oxidation. Chromatographic profiles of the oils from C. validus, as well as the plant organs were generated using gas chromatography-mass spectroscopy (GC-MS). Predominant compounds present in the oil included alpha-Cubebene, Camphene, Geraniol, Limonene, Myrcene, Palmitic acid and Sabinene. C. validus essential oil was also investigated for its antimicrobial (disk diffusion), antioxidant (1, 1-Diphenyl-1-Picrylhydrazyl (DPPH) assay), anti-inflammatory (5-lipoxygenase assay), anti-mosquito properties (insecticidal, larvicidal and repellency assays) and toxicity profile (Brine shrimp and Ames assays). The oil showed poor antimicrobial activity and inhibited the growth of only Gram positive bacteria with a minimum inhibitory concentration (MIC) of 0.0625 (vol/vol) for Bacillus, Micrococcus and Staphylococcus species. The oil also exhibited excellent antioxidant activity, scavenging more than 80% of DPPH free radicals and possesses anti-inflammatory activity (IC50=190 ppm). C. validus oil showed good adulticidal activity (53.7% mortality) and excellent larvicidal (100% mortality) and repellent activity (100% repellency) against Anopheles arabiensis mosquitoes. At high concentrations, the oil was toxic to brine shrimp larvae. However, when diluted it was safe and the minimum inhibitory concentration was 0.0001(vol/vol). The absence of revertant colonies at all essential oil concentrations in the Ames test suggest that the oil is not mutagenic. These results lead the way for exploiting C. validus oil as a multi-functional agent that has antibacterial, anti-oxidant, anti-inflammatory, and anti-mosquito properties.