Characterization of polychlorinated alkane mixtures—a Monte Carlo modeling approach

A Monte Carlo model was developed to characterize the molecular composition of polychlorinated alkane mixtures. The model is based upon a simulation of the free-radical chlorination process by which polychlorinated alkane mixtures are produced industrially from n-alkanes. In the model, the free-radical chlorination reaction was simulated by randomly selecting a position on a partially converted alkane molecule for target by chlorine free-radical attack. The relative reactivities of the hydrogen atoms on the alkane chain towards chlorine free-radical substitution were either determined experimentally or extrapolated from experimental results and incorporated into the model. The result of the simulation is the prediction of the detailed molecular composition of any PCA mixture. Good agreement was found when comparing the distribution of molecules predicted by the model to analytically determined distributions of real PCA mixtures. Results from the model were then coupled with rules describing the action of biological enzymes to estimate the upper limit possible for the aerobic biodegradation of PCA mixtures.     

The structure of the exocellular polysaccharide produced by Rhodococcus sp. RHA1

Rhodococcus sp. RHA1 is a Gram-positive actinomycete capable of metabolizing a wide spectrum of organic compounds whose survival in chemically hostile environments is believed to be in part due to the production of an exocellular polysaccharide (EPS). In order to investigate the functional nature of the EPS, its structure was determined using a combinatory approach including hydrolysis, composition, and methylation, analysis methods, as well as 2D (1)H and (13)C NMR spectroscopy. The EPS was found to be a high-molecular-mass polymer of a repeating tetrasaccharide unit composed of D-glucuronic acid, D-glucose, D-galactose, L-fucose and O-acetyl (1:1:1:1:1), and has the structure:     

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.     

The significance of nasal carriage of Staphylococcus aureus as risk factor for human skin infections

The effects of 2,2',5,5'-tetrachlorobiphenyl (TeCB), a PCB congener, and biphenyl on the cytoplasmic membranes of Ralstonia eutropha H850 were investigated by measuring fluorescence polarization using 1,6-diphenyl-1,3,5-hexatriene (DPH) as the probe, and determining the cellular fatty acid compositions. TeCB significantly affected the membrane of R. eutropha H850 cells grown on fructose by decreasing DPH fluorescence polarization. In contrast, the membrane of cells grown on biphenyl showed a considerably less significant effect of TeCB on membrane polarization than in fructose-grown cells. An increase in the ratio of total saturated to unsaturated fatty acids in cells grown on biphenyl suggested less of a fluidizing effect of TeCB on membranes in those cells. When biphenyl-grown cells were transferred back to a fructose medium, they required 25 generations for the membrane polarization and fatty acid compositions of these cells to revert back to those of the initial fructose-grown cells. The re-adaptation to a change in temperature required only five generations to return to normal. These results show that biphenyl affects cells in more ways than simply fluidizing the cytoplasmic membrane.     

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.     

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.     

Flux control analysis for biphenyl metabolism by Rhodococcus pyridinovorans R04

The flux control coefficients of the four enzymes involved in the upper pathway of biphenyl degradation were determined from transient metabolite concentrations. The first enzyme was indicated as the major rate-limiting step of the pathway with a control coefficient of 0.48. The flux control coefficients of the other three enzymes were 0.03, 0.23 and 0.27, respectively. This is the first experimental evidence of the control step in the pathway of biphenyl degradation using metabolic control analysis.     

A Thermostable Xylanase from a Thermophilic Acidophilic Bacillus sp.

Bacillus sp. 11-IS, a strain of thermophilic acidophilic bacteria, produced an extracellular xylanase during growth on xylan. The enzyme purified from the culture supernatant solution was homogeneous on disc-gel electrophoresis. The molecular weight was calculated to be 56,000 by SDS-gel electrophoresis. The enzyme had a pH optimum for activity at 4.0, and its stability range was pH 2.0 ~ 6.0. The temperature optimum was 80°C (10-min assay); however, the enzyme retained full activity after incubation at 70°C for 15 min. The enzyme acted on carboxymethyl cellulose (CMC) and cellulose, as well as on xylan. The Michaelis constants for larchwood xylan and CMC were calculated to be 1.68 mg xylose eq/ml and 0.465 mg glucose eq/ml, respectively. The predominant hydrolysis products from larchwood xylan were xylobiose, xylotriose, and xylose; the release of arabinose from rice-straw arabinoxylan was not detected. CMC was cleaved to cellobiose and larger oligosaccharides. Thus, the enzyme is considered to be an endoenzyme which degrades the β-1,4-glycosyl linkages in xylan and cellulose.     

Aromatic hydrocarbon degradation by Sphingomonas yanoikuyae B1

Sphingomonas yanoikuyae B1 is able to grow on a wide variety of aromatic compounds including biphenyl, naphthalene, phenanthrene, toluene, m-, and p-xylene. In addition, the initial enzymes for degradation of biphenyl have the ability to metabolize a wide variety of different polycyclic aromatic hydrocarbons. The catabolic pathways for the degradation of both the monocyclic and polycyclic aromatic hydrocarbons are intertwined, joining together at the level of (methyl)benzoate and catechol. Both upper branches of the catabolic pathways are induced when S. yanoikuyae B1 is grown on either class of compound. An analysis of the genes involved in the degradation of these aromatic compounds reveals that at least six operons are involved. The genes are not arranged in discrete pathway units but are combined in groups with genes for the degradation of both classes of compounds in the same operon. Genes for multiple dioxygenases are present perhaps explaining the ability of S. yanoikuyae B1 to grow on a wide variety of aromatic compounds. Received 10 August 1997/ Accepted in revised form 15 August 1997