Computational identification and analysis of functional polymorphisms involved in the activation and detoxification genes implicated in endometriosis

Endometriosis is a complex disorder of the female reproductive system where endometrial tissue embeds and grows at extrauterine location leading to inflammation and pain. Hundreds of polymorphisms in several genes have been studied as probable risk factors of this debilitating disease. Bioinformatics tools have come a long way in augmenting the search for putative functional polymorphisms in human diseases. In this study we have explored 16 genes involved in the detoxification of xenobiotic chemicals that are implicated in endometriosis by utilising publically available programs like SIFT, Polyphen, Panther, FastSNP, SNPeffect and PhosSNP. The variations among different ethnic populations of the SNPs were studied. We then calculated the extent to which bioinformatics based predictions are concurrent with real world epidemiological, genotyping studies using a set of SNPs that have been studied in endometriosis case–control studies. Our study shows that there is a significant positive correlation (r = 0.569, p < 0.005) between the summary of the predicted scores taken from 4 different servers and the odds ratio found from epidemiological studies. This report has identified and catalogued various deleterious SNPs that could be important in endometriosis and could aid in further analysis by in vitro and in vivo methods for the better understanding of the disease pathophysiology.     

Uncertainty in Multi-Pathway Risk Assessment for Combustion Facilities

Multi-pathway risk assessments (MPRAs) of contaminant emissions to the atmosphere consider both direct exposures, via ambient air, and indirect exposures, via deposition to land and water. MPRAs embody numerous interconnected models and parameters. Concatenation of many multiplicative and incompletely defined assumptions and inputs can result in risk estimates with considerable uncertainties, which are difficult to quantify and elucidate. Here, three MPRA case-studies approach uncertainties in ways that better inform context-specific judgments of risk. In the first case, default values predicted implausibly large impacts; substitution of site-specific data within conservative methods resulted in reasonable and intuitive worst-case estimates. In the second, a simpler, clearly worst-case water quality model sufficed to demonstrate acceptable risks. In the third case, exposures were intentionally and transparently overestimated. Choices made within particular MPRAs depend on availability of data as suitable replacements for default assumptions, regulatory requirements, and thoughtful consideration of the concerns of interested stakeholders. Explicit consideration of the biases inherent in each risk assessment lends greater credibility to the assessment results, and can form the bases for evidence-based decision-making.     

Biodegradation of PCBs in two-phase partitioning bioreactors following solid extraction from soil

This article demonstrates the feasibility of a novel process concept for the remediation of PCB contaminated soil. The proposed process consists of PCB extraction from soil using solid polymer beads, followed by biodegradation of the extracted PCBs in a solid-liquid two-phase partitioning bioreactor (TPPB), where PCBs are delivered from the polymer beads to the degrading organisms. The commercially available thermoplastic polymer Hytrel was used to extract Aroclor 1242 from contaminated artificial soil in bench scale experiments. Initial PCB contamination levels of 100 and 1,000 mg kg(-1) could be reduced to 32% +/- 1 to 41% +/- 7 of the initial value after 48 h mixing in the presence of a mobilizing agent at polymer-to-soil ratios of 1% (w/w) and 10% (w/w). The decrease of detectable PCBs in the soil was consistent with an increase of PCBs in the polymer beads. It was further shown that Aroclor 1242 could be delivered to the PCB degrading organism Burkholderia xenovorans LB400 in a solid-liquid TPPB via Hytrel beads. A total of 70 mg Aroclor 1242 could be degraded in a 1 L solid-liquid TPPB within 80 h of operation.     

Enhancement of PCB degradation by Burkholderia xenovorans LB400 in biphasic systems by manipulating culture conditions

Two-phase partitioning bioreactors (TPPBs) can be used to biodegrade environmental contaminants after their extraction from soil. TPPBs are typically stirred tank bioreactors containing an aqueous phase hosting the degrading microorganism and an immiscible, non-toxic and non-bioavailable organic phase functioning as a reservoir for hydrophobic compounds. Biodegradation of these compounds in the aqueous phase results in thermodynamic disequilibrium and partitioning of additional compounds from the organic phase into the aqueous phase. This self-regulated process can allow the delivery of large amounts of hydrophobic substances to degrading microorganisms. This paper explores the reactor conditions under which the polychlorinated biphenyl (PCB) degrader Burkholderia xenovorans LB400 can degrade significant amounts of the PCB mixture Aroclor(R) 1242. Aroclor(R) degradation was found to stall after approximately 40 h if no carbon source other than PCBs was available in the reactor. Sodium pyruvate was found to be a suitable carbon source to maintain microbial activity against PCBs and to function as a substrate for additional cell growth. Both biphenyl (while required during the inoculum preparation) and glucose had a negative effect during the Aroclor(R) degradation phase. Initial Aroclor(R) 1242 degradation rates in the presence of pyruvate were high (6.2 mg L(-1) h(-1)) and 85% of an equivalent concentration of 100 mg Aroclor(R) 1242 per L aqueous phase could be degraded in 48 h, which suggest that solvent extraction of PCBs from soil followed by their biodegradation in TPPBs might be a feasible remediation option.     

The reductive dechlorination of 2,3,4,5-tetrachlorobiphenyl in three different sediment cultures: evidence for the involvement of phylogenetically similar Dehalococcoides-like bacterial populations

Anaerobic cultures capable of reductively dechlorinating 2,3,4,5-tetrachlorobiphenyl (CB) were enriched from three different sediments, one estuarine, one marine and one riverine. Two different electron donors were used in enrichments with the estuarine sediment (elemental iron or a mixture of fatty acids). The removal of doubly flanked meta and para chlorines to form 2,3,5-CB and 2,4,5-CB was observed in all cultures. Bacterial community analysis of PCR-amplified 16S rRNA gene fragments revealed different communities in these cultures, with the exception of one common population that showed a high phylogentic relatedness to Dehalococcoides species. No Dehalococcoides-like populations were ever detected in control cultures to which no PCBs were added. In addition, the dynamics of this Dehalococcoides-like population were strongly correlated with dechlorination. Subcultures of the estuarine sediment culture demonstrated that the Dehalococcoides-like population disappeared when dechlorination was inhibited with 2-bromoethanesulfonate or when 2,3,4,5-CB had been consumed. These results provide evidence that Dehalococcoides-like populations were involved in the removal of doubly flanked chlorines from 2,3,4,5-CB. Furthermore, the successful enrichment of these populations from geographically distant and geochemically distinct environments indicates the widespread presence of these PCB-dechlorinating, Dehalococcoides-like organisms.     

Crystallization and preliminary crystallographic analysis of a 2,3-dihydroxybiphenyl dioxygenase from Pseudomonas sp. strain KKS102 having polychlorinated biphenyl (PCB)-degrading activity

Crystals have been obtained for a 2,3-dihydroxybiphenyl dioxygenase (conventionally called BphC) from a polychlorinated biphenyl (PCB)-degrader, Pseudomonas sp. strain KKS1O2. The crystals were grown using both ammonium sulfate and MPD as the precipitating agents. The crystals belonged to a tetragonal space group (I422) and diffracted to 2.5 Å. © 1995 Wiley-Liss, Inc.     

Interactions between the active metabolite of tryptophan pyrolysate mutagen, N-hydroxy-Trp-P-2, and lipids: the role of lipid peroxides in the conversion of N-hydroxy-Trp-P-2 to non-reactive forms

The interactions between lipids and the mutagenic active metabolite of 3-amino-1-methyl-5H-pyrido[4,3-b]indole (Trp-P-2) and 3-hydroxyamino-1-methyl-5H-pyrido[4,3-b]indole (N-hydroxy-Trp-P-2), were studied. Oleic acid showed an inhibitory effect on the formation of this active metabolite mainly by inhibition of hepatic microsomal oxidation systems. On the other hand, microsomal lipids from rat liver and commercial pig liver lecithin diminished the amount of N-hydroxy-Trp-P-2 without inhibiting the metabolism of Trp-P-2. The direct reaction of these lipids with N-hydroxy-Trp-P-2 was disclosed by experiments using N-hydroxy-Trp-P-2 and lipids without microsomes. Furthermore, the participation of lipid peroxides in this reaction was suggested by a linear relationship between the concentrations of the conjugated diene of lipids and the disappearance of N-hydroxy-Trp-P-2. When [3H]N-hydroxy-Trp-P-2 was incubated in the presence of pig liver lecithin, the polar products which were not formed in the incubation without lipids were newly detected by thin-layer chromatography (TLC) analysis.     

Polybrominated biphenyls as aryl hydrocarbon hydroxylase inducers: structure-activity correlations

The synthesis of all possible laterally-substituted polybrominated biphenyl (PBB) congeners containing two para bromines is described. Using enzymic, electrophoretic and ligand-binding assays that distinguish between phenobarbitone(PB)- and 3-methylcholanthrene(MC)-type inducers, the synthetic PBBs were evaluated as inducers of liver microsomal drug-metabolizing enzymes in the immature male Wistar rat. 4,4'-Dibromobiphenyl resembled PB in its mode of induction whereas all the meta-brominated derivatives of 4,4'-dibromobiphenyl, namely 3,4,4'-tri, 3,4,4',5-tetra-, 3,3', 4,4'-tetra-, 3,3',4,4',5-penta- and 3,3',4,4',5,5'-hexabromobiphenyl, resembled MC in their mode of induction. The results obtained with 3,4,4'-tribromobiphenyl demonstrate that, in contrast to the polychlorinated biphenyls (PCBs), a single meta halogen substituent is sufficient to abolish the PB-type characteristics of 4,4'-dibromobiphenyl and convert it to a strictly MC-type inducer. PBBs which induce AHH activity must be substituted at both para positions and at one, two, three or four meta positions. Ortho-substitution of PBBs which contain only lateral bromine groups may also give compounds which are aryl hydrocarbon hydroxylase (AHH) inducers. One of the MC-type PBBs, namely 3,3',4,4'-tetrabromobiphenyl, which has been tentatively identified in the commercial PBB mixture, fireMaster BP-6, was at least 50 times more potent as an inducer of AHH activity than the commercial PBB mixture. The induction of AHH by 3,3',4,4'-tetrabromobiphenyl was accompanied by a dose-dependent decrease in both thymus and spleen weights. The thymus and/or spleen weights were decreased in rats treated with the other MC-type PBBs which further supports the correlation between the toxicity of the PBBs and their ability to induce AHH.