Cytochrome P450 enzymes (CYPs), found in almost all organisms, are involved in endobiotic metabolism and detoxification of xenobiotic compounds, such as drugs, pollutants, and insecticides. In insects, CYPs play a major role in conferring resistance to various insecticides including DDT. In Drosophila and other insects, DDT-resistant strains exhibit increased expression of multiple P450 genes; however, the mechanism of overexpression is unknown. Since many CYP genes including Cyp6a8 of Drosophila are induced by caffeine and other xenobiotics, these chemicals are used as tools to understand the regulation of these genes. Previously it was shown that the 0.8-kb (-1/-732) and 0.2-kb (-1/-170) upstream DNA of Cyp6a8 of the DDT-resistant 91-R strain support caffeine, DDT, and Phenobarbital induction in adult flies and S2 cells, the 0.2-kb DNA has many transcriptionally important sequence motifs. In the present investigation, site-directed mutagenesis was performed on the putative TATA box and CREB/AP-1 motifs located at the -97/-101, -57/-61, -43/-47, and -6/-10 regions of the 0.2- and 0.8 DNAs to determine their cis-regulatory role in caffeine and PB induction in S2 cells using luciferase reporter system. Results showed that all four deletions in 0.2- and 0.8-kb DNA decreased both basal and caffeine-induced activities, but maximum effect was seen with the -57/-61 deletion. Second, the TATA mutations greatly decreased basal activity, but they did not decrease caffeine-inducibility as much as the -57/-61 mutations. Third, the effects of other three deletions on basal activities were not as pronounced in the 0.8-kb environment as were seen in the 0.2-kb environment. Taken together these results suggest that of all four putative CREB/AP1 sites the one located at -57/-61 region is most important for both basal and caffeine-induced activities. The results also suggest that the additional 600 bases upstream of -1/-170 have distal elements that interact with the proximal promoter in the 0.2-kb DNA and boost basal transcription. A model suggesting interactions of all cis elements with the basal promoter for basal and induced transcription has been proposed.

No description available.

In this dissertation, the intermolecular interactions between soil organic matter (SOM) and organofluorine compounds have been studied at the molecular-level using Nuclear Magnetic Resonance (NMR) spectroscopy. NMR probes the local magnetic environment surrounding atomic nuclei, and is uniquely capable as an analytical tool to probe molecular environments in complex disordered materials, such as soils. Several NMR techniques were employed in this work, including Pulse Field Gradient (PFG)-NMR based diffusion measurements, solid-state cross-polarization (CP), saturation transfer difference (STD) spectroscopy, and reverse-heteronuclear saturation transfer difference (RHSTD) spectroscopy. Using organofluorine compounds as molecular probes, xenobiotic interactions with SOM were studied. Using 1H{19F} RHSTD, the interaction sites in humic acid for organofluorine compounds were identified by direct molecular-level methods. Protein and lignin were identified as major binding sites, with different preferences exhibited for these sites by dissimilar organofluorine compounds: aromatic organofluorine compounds display varied preference for aromatic humic acid sites while perfluorooctanoic acid exhibits near total selectivity for protein-derived binding sites. The mechanisms underlying these preferences were probed in the solution state. Using crucial knowledge from the humic acid studies, a detailed molecular-level investigation of xenobiotic interactions in an intact and unmodified whole soil was made possible. A direct and in situ elucidation of the components in soil organic matter that interact with small organofluorine xenobiotic molecules has been presented, allowing, for the first time, resolution of multiple interactions occurring for xenobiotics simultaneously at different sites within a whole soil.

In this dissertation, the intermolecular interactions between soil organic matter (SOM) and organofluorine compounds have been studied at the molecular-level using Nuclear Magnetic Resonance (NMR) spectroscopy. NMR probes the local magnetic environment surrounding atomic nuclei, and is uniquely capable as an analytical tool to probe molecular environments in complex disordered materials, such as soils. Several NMR techniques were employed in this work, including Pulse Field Gradient (PFG)-NMR based diffusion measurements, solid-state cross-polarization (CP), saturation transfer difference (STD) spectroscopy, and reverse-heteronuclear saturation transfer difference (RHSTD) spectroscopy. Using organofluorine compounds as molecular probes, xenobiotic interactions with SOM were studied. Using 1H{19F} RHSTD, the interaction sites in humic acid for organofluorine compounds were identified by direct molecular-level methods. Protein and lignin were identified as major binding sites, with different preferences exhibited for these sites by dissimilar organofluorine compounds: aromatic organofluorine compounds display varied preference for aromatic humic acid sites while perfluorooctanoic acid exhibits near total selectivity for protein-derived binding sites. The mechanisms underlying these preferences were probed in the solution state. Using crucial knowledge from the humic acid studies, a detailed molecular-level investigation of xenobiotic interactions in an intact and unmodified whole soil was made possible. A direct and in situ elucidation of the components in soil organic matter that interact with small organofluorine xenobiotic molecules has been presented, allowing, for the first time, resolution of multiple interactions occurring for xenobiotics simultaneously at different sites within a whole soil.

>Magister Scientiae - MSc / The human arylamine N-acetyltransferase 1 (NAT1) is critical in determining the duration of action and pharmacokinetics of amine-containing drugs such as para-aminosalicylic acid and para-aminobenzoyl glutamate used in clinical therapy of tuberculosis (TB), as well as influencing the balance between detoxification and metabolic activation of these drugs. SNPs in this enzyme are continuously being detected and indicate inter-ethnic and inter-individual variation in the enzyme function. The effect of nsSNPs on the structure and function of proteins are routinely analyzed using SIFT and POLYPHEN-2 prediction algorithms. The false-negative rate of these two algorithms results in as much as 25% of nsSNPs. This study aimed to explore the use of homology modeling including residue interactions, Gibbs free energy change and solvent accessibility as additional evidence for predicting nsSNP effects on enzyme function.This study evaluated the functional effects of 14 nsSNPs identified in a South African mixed ancestry population of which 3 nsSNPs were previously identified in Caucasians. The SNPs were evaluated using structural analysis that included homology modeling, residue interactions, relative solvent accessibility,Gibbs free energy change and sequence conservation in addition to the routinely used nsSNP function prediction algorithms, SIFT and POLYPHEN-2. The structural analysis implemented in this study showed a loss of hydrogen bonds for S259R thereby affecting protein function which contradicts predictions obtained from SIFT and POLYPHEN-2 algorithms. The variant N245I was shown to be neutral but contradicted the predictions from SIFT and POLYPHEN-2. Structural analysis predicted that variant R242M would affect protein stability and therefore NAT1 function in agreement with POLYPHEN-2 predictions but contradicting predictions from SIFT. No structural changes were expected for variant E264K in agreement with predictions obtained from POLYPHEN-2 but contradicting results from SIFT. The functions of the remaining 10 nsSNPs were consistent with those predicted by SIFT and POLYPHEN-2 namely that four variants R117T, E167Q, T193S and T240S do not affect the NAT1 function whereas R166T, F202V, Q210P, D229H, V231G and V235A could affect the enzyme function.This study provided the first evaluation of the functional effects of 11 newly characterized nsSNPs on the NAT1 tuberculosis drug-metabolizing enzyme. The six functionally important nsSNPs predicted by all three methods and the four SNPs with contradictory results will be tested experimentally by creating a SNP construct that will be cloned into an expression vector. These combined computational and experimental studies will advance our understanding of NAT1 structure-function relationships and allow us to interpret the NAT1 genetic polymorphisms in individuals who are slow or fast acetylators. The results, albeit a small dataset demonstrate that the routinely used algorithms are not without flaws and that improvements in functional prediction of nsSNPs can be obtained by close scrutiny of the molecular interactions of wild type and variant amino acids.

This diploma thesis was focused on studying the interaction of humic substances with ionic organic xenobiotics and its structural aspects. The method was chosen from my bachelor thesis, steady-state fluorescence spectroscopy, which is suitable for substances with weak fluorescence. The results showed that the interaction between humic acids and representatives of ionic organic xenobiotics (Septonex) was reflected in fluorescence quenching of humic acids and the shift of emission maximum to lower wavelength, hypsochromic (blue) shift. From the measurement results, we can assume that the interaction that is formed between the aromatic structures in humic acids and Septonex could be -cation interaction.

The worldwide rise of diabetes and obesity has spurred research investigating the molecular mechanisms that mediate the deleterious effects associated with these diseases. Individuals with diabetes and/or obesity are at increased risk from a variety of health consequences, including heart attack, stroke and peripheral vascular disease; all of these complications have oxygen deprivation as the central component of their pathology. The nematode Caenorhabditis elegans has been established as a model system for understanding the genetic and molecular regulation of oxygen deprivation response, and in recent years methods have been developed to study the effects of excess glucose and altered lipid homeostasis. Using C. elegans, I investigated transcriptomic profiles of wild-type and hyl-2(tm2031) ( a ceramide biosynthesis mutant) animals fed a standard or a glucose supplemented diet. I then completed a pilot RNAi screen of differentially regulated genes and found that genes involved in the endobiotic detoxification pathway (ugt-63 and cyp-25A1) modulate anoxia response. I then used a lipidomic approach to determine whether glucose feeding or mutations in the ceramide biosynthesis pathway or the insulin-like signaling pathway impact lipid profiles. I found that gluocose alters the lipid profile of daf-2(e1370) (an insulin-like receptor mutant) animals. These studies indicate that a transcriptomic approach can be used to discover novel pathways involved in oxygen deprivation response and further validate C. elegans as a model for understanding diabetes and obesity.

<p>CYPs are a large and diverse protein superfamily found in all domains of life and are able to metabolize a wide array of both exogenous and endogenous molecules. The CYPome of the polychaete annelid Capitella teleta has been robustly identified and annotated with the genome assembly available (version 1). Annotation of 84 full length and 12 partial CYP sequences predicted a total of 96 functional CYPs in C. teleta. A further 13 CYP fragments were found but these may be pseudogenes. The C. teleta CYPome contained 24 novel CYP families and seven novel CYP subfamilies within existing families. A phylogenetic analysis was completed, primarily with vertebrate sequences, and identified that the C teleta sequences were found in 9 of the 11 metazoan CYP clans. Clan 2 was expanded in this species with 51 CYPs in 14 novel CYP families containing 20 subfamilies. There were five clan 3, four clan 4, and six mitochondrial clan full length CYPs. Two CYPs, CYP3071A1 and CYP3072A1, did not cluster with any metazoan CYP clan. C. teleta had a CYP51A1 gene with ~65% identity to vertebrate CYP51A1 sequences and was predicted to have lanosterol 14 α-demethylase activity. Several CYPs (CYP376A1, CYP3068A1, CYP3069A1, and CYP3070A1) are discussed as candidate genes for steroidogenesis. There are two CYP1-like CYPs and a total of four CYP331s found in C. teleta, which may play a role in PAH metabolism and warrant further analysis.</p> / Master of Science (MSc)

Neste estudo avaliou-se a remoção e degradação de surfactante aniônico linear alquilbenzeno sulfonado (LAS) e compostos orgânicos xenobióticos em água residuária de lavanderia comercial em reator anaeróbio de leito fluidificado (RALF) preenchido com areia como material suporte, em escala de bancada (1,2 L), bem como a comunidade microbiana do biofilme e biomassa do separador de fases ao final da operação. O reator foi inoculado com lodo proveniente de reator UASB utilizado no tratamento de dejetos de suinocultura e alimentado com substrato sintético acrescido de água residuária de lavanderia comercial. Caracterização da água residuária, análises de monitoramento da concentração de LAS e matéria orgânica, além de outros parâmetros físico-químicos foram realizadas durante as etapas de operação do sistema. Essa operação foi dividida em cinco etapas: I adaptação da biomassa (575±28mg.L-1 de DQO), II (9,5±3 mg.L-1 de LAS e 637±80mg.L-1 de DQO), III (23,3±8mg.L-1 de LAS e 686±92 mg.L-1 de DQO), IV (21,7±10mg.L-1 de LAS e 691±103 mg.L-1 de DQO), V (27,9±9,6mg.L-1 de LAS e 666±161mg.L-1 de DQO). Aplicação das técnicas de PCR/DGGE e pirosequenciamento da região do rRNA 16S foi realizada para constatar a diversidade microbiana nas etapas IV (com sacarose) e V (sem sacarose). Por meio da caracterização da água residuária de lavanderia comercial foi evidenciado grande variação na concentração de diversos parâmetros, principalmente matéria orgânica (704 mg.L-1 a 4.830 mg.L-1) e LAS (12,2 mg.L-1 a 11.949 mg.L-1). A eficiência média de remoção de matéria orgânica e LAS foi 88% e 60%, respectivamente, durante toda operação do reator. As populações dos Domínios Archaea e Bacteria foram 54% e 45%, similares, respectivamente, para a biomassa da Etapa IV e Etapa V. Por meio da análise de pirosequenciamento das amostras das Etapas IV e V da areia e separador de fases do reator foram identificados 92 gêneros dos quais 24 foram relacionados com a degradação de LAS (Bdellovibrio, Ferruginibacter, Gemmatimonas, etc.). / In this study the removal and degradation of anionic surfactant linear alkylbenzene sulfonate (LAS) and xenobiotic organic compounds in a commercial laundry wastewater was evaluated in anaerobic fluidized bed reactor (AFBR) filled with sand as support material, in a bench scale (1, 2 L), as well as the microbial community of the biofime and phase separator biomass at the end of the operation. The reactor was inoculated with sludge from a UASB reactor used in the swine manure treatment and fed with synthetic substrate plus commercial laundry wastewater. Wastewater characterisation, monitoring analyzes of LAS, organic matter and other physico-chemical parameters were performed during the stages of system operation. This operation was divided into five stages: Stage I - biomass adaptation (575 ± 28mg L-1 of COD), Stage II (9.5 ± 3 mg L-1 of LAS and 637 ± 80 mg L-1 of COD ), Stage III (23.3 ± 8 mg L-1 of LAS and 686 ± 92 mg L-1 of COD), Stage IV (21.7 ± 10 mg L-1 of LAS and 691 ± 103 mg L-1 of COD), Stage V (27.9 ± 9.6 mg L-1 of LAS and 666 ± 161 mg L-1 of COD). Application of PCR/DGGE and pyrosequencing of the 16S rRNA region was performed to verify the microbial diversity in the operational phase IV (with sucrose) and V (without sucrose). Through the commercial laundry wastewater characterization a wide variation in several parameters concentration was shown, mainly organic matter (704mg L-1 to 4.830mg L-1) and LAS (12.2mg L-1 to 11.949mg L-1). The average removal efficiency of organic matter and LAS was 88% and 60%, respectively, throughout the reactor operation. The populations of the Archaea and Bacteria Domains were 54% and 45% similar, respectively, for Stages IV and V biomass. By pyrosequencing analysis of sand and phase separator samples from the Stages IV and V, 92 genera of which 24 were related to the degradation of LAS (Bdellovibrio, Ferruginibacter, Gemmatimonas, Holophaga, Magnetospirillum, Zoogloea, etc.) were identified.

Neste estudo avaliou-se a remoção e degradação de surfactante aniônico linear alquilbenzeno sulfonado (LAS) e compostos orgânicos xenobióticos em água residuária de lavanderia comercial em reator anaeróbio de leito fluidificado (RALF) preenchido com areia como material suporte, em escala de bancada (1,2 L), bem como a comunidade microbiana do biofilme e biomassa do separador de fases ao final da operação. O reator foi inoculado com lodo proveniente de reator UASB utilizado no tratamento de dejetos de suinocultura e alimentado com substrato sintético acrescido de água residuária de lavanderia comercial. Caracterização da água residuária, análises de monitoramento da concentração de LAS e matéria orgânica, além de outros parâmetros físico-químicos foram realizadas durante as etapas de operação do sistema. Essa operação foi dividida em cinco etapas: I adaptação da biomassa (575±28mg.L-1 de DQO), II (9,5±3 mg.L-1 de LAS e 637±80mg.L-1 de DQO), III (23,3±8mg.L-1 de LAS e 686±92 mg.L-1 de DQO), IV (21,7±10mg.L-1 de LAS e 691±103 mg.L-1 de DQO), V (27,9±9,6mg.L-1 de LAS e 666±161mg.L-1 de DQO). Aplicação das técnicas de PCR/DGGE e pirosequenciamento da região do rRNA 16S foi realizada para constatar a diversidade microbiana nas etapas IV (com sacarose) e V (sem sacarose). Por meio da caracterização da água residuária de lavanderia comercial foi evidenciado grande variação na concentração de diversos parâmetros, principalmente matéria orgânica (704 mg.L-1 a 4.830 mg.L-1) e LAS (12,2 mg.L-1 a 11.949 mg.L-1). A eficiência média de remoção de matéria orgânica e LAS foi 88% e 60%, respectivamente, durante toda operação do reator. As populações dos Domínios Archaea e Bacteria foram 54% e 45%, similares, respectivamente, para a biomassa da Etapa IV e Etapa V. Por meio da análise de pirosequenciamento das amostras das Etapas IV e V da areia e separador de fases do reator foram identificados 92 gêneros dos quais 24 foram relacionados com a degradação de LAS (Bdellovibrio, Ferruginibacter, Gemmatimonas, etc.). / In this study the removal and degradation of anionic surfactant linear alkylbenzene sulfonate (LAS) and xenobiotic organic compounds in a commercial laundry wastewater was evaluated in anaerobic fluidized bed reactor (AFBR) filled with sand as support material, in a bench scale (1, 2 L), as well as the microbial community of the biofime and phase separator biomass at the end of the operation. The reactor was inoculated with sludge from a UASB reactor used in the swine manure treatment and fed with synthetic substrate plus commercial laundry wastewater. Wastewater characterisation, monitoring analyzes of LAS, organic matter and other physico-chemical parameters were performed during the stages of system operation. This operation was divided into five stages: Stage I - biomass adaptation (575 ± 28mg L-1 of COD), Stage II (9.5 ± 3 mg L-1 of LAS and 637 ± 80 mg L-1 of COD ), Stage III (23.3 ± 8 mg L-1 of LAS and 686 ± 92 mg L-1 of COD), Stage IV (21.7 ± 10 mg L-1 of LAS and 691 ± 103 mg L-1 of COD), Stage V (27.9 ± 9.6 mg L-1 of LAS and 666 ± 161 mg L-1 of COD). Application of PCR/DGGE and pyrosequencing of the 16S rRNA region was performed to verify the microbial diversity in the operational phase IV (with sucrose) and V (without sucrose). Through the commercial laundry wastewater characterization a wide variation in several parameters concentration was shown, mainly organic matter (704mg L-1 to 4.830mg L-1) and LAS (12.2mg L-1 to 11.949mg L-1). The average removal efficiency of organic matter and LAS was 88% and 60%, respectively, throughout the reactor operation. The populations of the Archaea and Bacteria Domains were 54% and 45% similar, respectively, for Stages IV and V biomass. By pyrosequencing analysis of sand and phase separator samples from the Stages IV and V, 92 genera of which 24 were related to the degradation of LAS (Bdellovibrio, Ferruginibacter, Gemmatimonas, Holophaga, Magnetospirillum, Zoogloea, etc.) were identified.