Effect of Benzene, Toluene, Ethylbenzene, and p-Xylene (BTEX) Mixture on Biodegradation of Methyl tert-Butyl Ether (MTBE) and tert-Butyl Alcohol (TBA) by Pure Culture UC1

The effect of a BTEX mixture on the biodegradation of methyl tert-butyl ether (MTBE) and its degradation intermediate, tert-butyl alcohol (TBA) was investigated in the pure bacterial culture UC1, which has been identified to be a strain of the known MTBE-degrader PM1 based on greater than 99% 16S rDNA similarity. Several degradation studies were carried out on UC1 at three initial concentration levels of MTBE or TBA: 6-7; 15-17; and 40-45 mg/l, both with and without BTEX present cumulatively at about half of the MTBE or TBA molar mass in the system. The BTEX mixture was observed not to affect either the rate or the degradation lag period of MTBE or TBA degradation, except that the TBA degradation rate actually increased when BTEX was present initially in the highest concentration studies. When serving as the sole substrate, the MTBE degradation rate ranged from 48 +/- 1.2 to 200 +/- 7.0 mg(MTBE)/g(dw) h, and the TBA degradation rate from 140 +/- 18 to 530 +/- 70 mg(TBA)/g(dw) h. When present with BTEX, MTBE and TBA rates ranged from 46 +/- 2.2 to 210 +/- 14 and 170 +/- 28 to 780 +/- 43 mg(TBA)/g(dw) h, respectively. In studies where varying concentrations of TBA were present with 5 mg/l MTBE, both compounds were degraded simultaneously with no obvious preference for either substrate. In the highest concentration study of TBA with 5 mg/l MTBE, BTEX was also observed to increase the ultimate rate of TBA degradation. In addition to exploring the affect of BTEX, this study also provides general insight into the metabolism of MTBE and TBA by pure culture UC1.     

Involvement of a Novel Enzyme, MdpA, in Methyl tert-Butyl Ether Degradation in Methylibium petroleiphilum PM1

Methylibium petroleiphilum PM1 is a well-characterized environmental strain capable of complete metabolism of the fuel oxygenate methyl tert-butyl ether (MTBE). Using a molecular genetic system which we established to study MTBE metabolism by PM1, we demonstrated that the enzyme MdpA is involved in MTBE removal, based on insertional inactivation and complementation studies. MdpA is constitutively expressed at low levels but is strongly induced by MTBE. MdpA is also involved in the regulation of tert-butyl alcohol (TBA) removal under certain conditions but is not directly responsible for TBA degradation. Phylogenetic comparison of MdpA to related enzymes indicates close homology to the short-chain hydrolyzing alkane hydroxylases (AH1), a group that appears to be a distinct subfamily of the AHs. The unique, substrate-size-determining residue Thr⁵⁹ distinguishes MdpA from the AH1 subfamily as well as from AlkB enzymes linked to MTBE degradation in Mycobacterium austroafricanum.     

Naturally occurring bacteria similar to the methyl tert-butyl ether (MTBE)-degrading strain PM1 are present in MTBE-contaminated groundwater

Methyl tert-butyl ether (MTBE) is a widespread groundwater contaminant that does not respond well to conventional treatment technologies. Growing evidence indicates that microbial communities indigenous to groundwater can degrade MTBE under aerobic and anaerobic conditions. Although pure cultures of microorganisms able to degrade or cometabolize MTBE have been reported, to date the specific organisms responsible for MTBE degradation in various field studies have not be identified. We report that DNA sequences almost identical (99% homology) to those of strain PM1, originally isolated from a biofilter in southern California, are naturally occurring in an MTBE-polluted aquifer in Vandenberg Air Force Base (VAFB), Lompoc, California. Cell densities of native PM1 (measured by TaqMan quantitative PCR) in VAFB groundwater samples ranged from below the detection limit (in anaerobic sites) to 10(3) to 10(4) cells/ml (in oxygen-amended sites). In groundwater from anaerobic or aerobic sites incubated in microcosms spiked with 10 microg of MTBE/liter, densities of native PM1 increased to approximately 10(5) cells/ml. Native PM1 densities also increased during incubation of VAFB sediments during MTBE degradation. In controlled field plots amended with oxygen, artificially increasing the MTBE concentration was followed by an increase in the in situ native PM1 cell density. This is the first reported relationship between in situ MTBE biodegradation and densities of MTBE-degrading bacteria by quantitative molecular methods.     

Induction of Methyl Tertiary Butyl Ether (MTBE)-Oxidizing Activity in Mycobacterium vaccae JOB5 by MTBE

Alkane-grown cells of Mycobacterium vaccae JOB5 cometabolically degrade the gasoline oxygenate methyl tertiary butyl ether (MTBE) through the activities of an alkane-inducible monooxygenase and other enzymes in the alkane oxidation pathway. In this study we examined the effects of MTBE on the MTBE-oxidizing activity of M. vaccae JOB5 grown on diverse nonalkane substrates. Carbon-limited cultures were grown on glycerol, lactate, several sugars, and tricarboxylic acid cycle intermediates, both in the presence and absence of MTBE. In all MTBE-containing cultures, MTBE consumption occurred and tertiary butyl alcohol (TBA) and tertiary butyl formate accumulated in the culture medium. Acetylene, a specific inactivator of alkane- and MTBE-oxidizing activities, fully inhibited MTBE consumption and product accumulation but had no other apparent effects on culture growth. The MTBE-dependent stimulation of MTBE-oxidizing activity in fructose- and glycerol-grown cells was saturable with respect to MTBE concentration (50% saturation level = 2.4 to 2.75 mM), and the onset of MTBE oxidation in glycerol-grown cells was inhibited by both rifampin and chloramphenicol. Other oxygenates (TBA and tertiary amyl methyl ether) also induced the enzyme activity required for their own degradation in glycerol-grown cells. Presence of MTBE also promoted MTBE oxidation in cells grown on organic acids, compounds that are often found in anaerobic, gasoline-contaminated environments. Experiments with acid-grown cells suggested induction of MTBE-oxidizing activity by MTBE is subject to catabolite repression. The results of this study are discussed in terms of their potential implications towards our understanding of the role of cometabolism in MTBE and TBA biodegradation in gasoline-contaminated environments.     

Response of Bdellovibrio and Like Organisms (BALOs) to the Migration of Naturally Occurring Bacteria to Chemoattractants

A dual culture-based and non–culture-based approach was applied to characterize predator bacterial groups in surface water samples collected from Apalachicola Bay, Florida. Chemotaxis drop assays were performed on concentrated samples in an effort to isolate predator bacteria by their chemotactic ability. Yeast extract (YE) and casamino acids (CA) proved to be strong chemoattractants and resulted in three visibly distinct bands; however, dextrose, succinate, pyruvate, and concentrated cells of Vibrio parahaemolyticus P5 as prey did not elicit any response. The three distinct bands from YE and CA were separately collected to identify the chemotactic microbial assemblages. Plaque-forming unit assays from different chemotaxis bands with P5 as prey indicated 5- (CA) to 10-fold (YE) higher numbers of predator bacteria in the outermost chemotactic bands. Polymerase chain reaction–restriction fragment length polymorphism and 16S rDNA sequencing of clones from different chemotaxis bands resulted in identification of Pseudoalteromonas spp., Marinomonas spp., and Vibrio spp., with their numbers inversely proportional to the numbers of predators—i.e., Bdellovibrio spp. and Bacteriovorax spp—in the chemotaxis bands. This study indicates that predatorial bacteria potentially respond to high densities of microbial biomass in aquatic ecosystems and that chemotaxis drop assay may be an alternate culture-independent method to characterize predatorial bacterial guilds from the environment.     

Sorption of Methyl tert -Butyl Ether (MTBE) and tert -Butyl Alcohol (TBA) to Hyporheic Zone Soils

Soil water distribution coefficients (K _d ) for methyl tert-butyl ether (MTBE) and its primary biodegradation intermediate tert-butyl alcohol (TBA) were determined for seven hyporheic zone soils ranging from 1 to 7% in organic carbon. Samples were collected in the area of the Spring Creek hyporheic zone in Ronan, Montana. Values for K _d ranged from 1.5 to 8.7 L kg^?1 for MTBE and from 0.15 to 0.41 L kg^?1 for TBA, and were highly correlated to the organic carbon content of the solids. However, for TBA the use of non-linear K _F values is more appropriate based on the results obtained, and the value of K _OC is calculated based on linear K _d transformation of the data. Distribution coefficients normalized to the fraction of organic carbon (log K _OC ) for MTBE and TBA were determined to be 2.13 ± 0.060 and 0.762 ± 0.088, respectively.     

A Field Application of Hydrogen-Releasing Compound (HRCTM) for the Enhanced Bioremediation of Methyl Tertiary Butyl Ether (MTBE)

Due to a greater understanding of the behavior of the fuel oxygenate Methyl Tertiary Butyl Ether (MTBE) in groundwater, the United States Environmental Protection Agency (EPA) and the American Petroleum Institute (API) recently have acknowledged the need for the development and application of additional remedial strategies to address the more extensive, longer lived, and faster moving dissolved MTBE plumes often associated with oxygenated fuel releases (API, 2000 and USEPA, 2000a). The need for alternative methods for managing dissolved MTBE plumes is particularly evident in the case of the Upper Glacial aquifer of Long Island, New York. Hydrogeologic conditions in the this water table aquifer (i. e., high hydraulic conductivity, high average pore velocities, low organic carbon, and high rates of recharge) have been found to contribute to the formation of extensive, long, narrow, and three-dimensional dissolved MTBE plumes that plunge into the aquifer in response to recharge (Weaver et. al. 1999). The characteristics of MTBE plumes in the Upper Glacial aquifer in combination with abundant sensitive receptors (mainly drinking water supply wells), often renders monitored natural attenuation (MNA) plume management strategies inappropriate, resulting in the need for plume control, frequently via pumping and treating (NYSDEC, 2000). In such cases, remedial costs can rise well beyond those associated with similar fuel releases that did not contain MTBE (USEPA, 1998a). Consequently, the application of remedial technologies for MTBE other than MNA, or pumping and treating, are of great interest to those responsible for the management of dissolved MTBE plumes on Long Island or in similar hydrogeologic settings. An alternative strategy for the remediation of dissolved MTBE plumes was recently field tested at an oxygenated fuel spill site on Long Island. The strategy was enhanced biodegradation via the application of Hydrogen Release Compound (HRC^TM). HRC^TM is a form of polylactate ester that slowly releases biodegradation stimulating constituents into the aquifer and has been shown in other studies to foster methanogenic conditions that advance the reductive dechlorina-tion of perchloroethene (PCE) and trichloroethene (TCE) (Koenigsberg, 1998). Numerous reports have been written that discuss the biodegradation of MTBE under aerobic conditions, as well as microcosm studies in which MTBE biodegradation was observed under anaerobic conditions. However, there are limited reports that document the natural anaerobic biodegradation of dissolved MTBE (McLoughlin, 2000). Despite the lack of documented natural anaerobic biodegradation of MTBE, it has been observed that MTBE transport often occurs under anoxic conditions at oxygenated fuel releases as the result of the biodegradation of other fuel constituents, such as benzene, toluene, ethylbenzene and xylene (BTEX), which deplete the available dissolved oxygen as well as other electron acceptors (nitrate, ferric iron, manganese, etc.) (USEPA, 2000c and API, 1996). Therefore, an anaerobic biodegradation strategy is attractive due to its synergy with the existing geochemical conditions. Consequently, the study was conceived and designed to test the ability of HRC(tm) to foster the anaerobic bio-degradation of MTBE under methano-genic conditions (McLoughlin, 2000). The application of HRC(tm) did result in the formation of a large area of enhanced reducing conditions in the vicinity and down gradient of the application zone. However, under these site conditions, the HRC(tm) application did not induce measurable methanogenic conditions with the associated elevated dissolved hydrogen concentrations required for significant MTBE anaerobic biodegradation. The high hydraulic conductivity and high average pore velocity at the site were likely responsible. Despite this, the study can be viewed as a success since much was learned that can be used in future studies of anaerobic biodegradation of MTBE and the application of HRC(tm).     

Naturally Occurring Mutations Alter the Stability of Polycystin-1 Polycystic Kidney Disease (PKD) Domains

Mutations in polycystin-1 (PC1) can cause autosomal dominant polycystic kidney disease, which is a leading cause of renal failure. The available evidence suggests that PC1 acts as a mechanosensor, receiving signals from the primary cilia, neighboring cells, and extracellular matrix. PC1 is a large membrane protein that has a long N-terminal extracellular region (about 3000 amino acids) with a multimodular structure including 16 Ig-like polycystic kidney disease (PKD) domains, which are targeted by many naturally occurring missense mutations. Nothing is known about the effects of these mutations on the biophysical properties of PKD domains. Here we investigate the effects of several naturally occurring mutations on the mechanical stability of the first PKD domain of human PC1 (HuPKDd1). We found that several missense mutations alter the mechanical unfolding pathways of HuPKDd1, resulting in distinct mechanical phenotypes. Moreover, we found that these mutations also alter the thermodynamic stability of a structurally homologous archaeal PKD domain. Based on these findings, we hypothesize that missense mutations may cause autosomal dominant polycystic kidney disease by altering the stability of the PC1 ectodomain, thereby perturbing its ability to sense mechanical signals.     

Naturally Occurring Mutations in the PA Gene Are Key Contributors to Increased Virulence of Pandemic H1N1/09 Influenza Virus in Mice

We examined the molecular basis of virulence of pandemic H1N1/09 influenza viruses by reverse genetics based on two H1N1/09 virus isolates (A/California/04/2009 [CA04] and A/swine/Shandong/731/2009 [SD731]) with contrasting pathogenicities in mice. We found that four amino acid mutations (P224S in the PA protein [PA-P224S], PB2-T588I, NA-V106I, and NS1-I123V) contributed to the lethal phenotype of SD731. In particular, the PA-P224S mutation when combined with PA-A70V in CA04 drastically reduced the virus''s 50% mouse lethal dose (LD₅₀), by almost 1,000-fold.     

Identification of Methyl Halide-Utilizing Genes in the Methyl Bromide-Utilizing Bacterial Strain IMB-1 Suggests a High Degree of Conservation of Methyl Halide-Specific Genes in Gram-Negative Bacteria

Strain IMB-1, an aerobic methylotrophic member of the alpha subgroup of the Proteobacteria, can grow with methyl bromide as a sole carbon and energy source. A single cmu gene cluster was identified in IMB-1 that contained six open reading frames: cmuC, cmuA, orf146, paaE, hutI, and partial metF. CmuA from IMB-1 has high sequence homology to the methyltransferase CmuA from Methylobacterium chloromethanicum and Hyphomicrobium chloromethanicum and contains a C-terminal corrinoid-binding motif and an N-terminal methyltransferase motif. However, cmuB, identified in M. chloromethanicum and H. chloromethanicum, was not detected in IMB-1.     

Nitrous Oxide Reductase Genes (nosZ) of Denitrifying Microbial Populations in Soil and the Earthworm Gut Are Phylogenetically Similar

Earthworms emit nitrous oxide (N₂O) and dinitrogen (N₂). It has been hypothesized that the in situ conditions of the earthworm gut activates ingested soil denitrifiers during gut passage and leads to these in vivo emissions (M. A. Horn, A. Schramm, and H. L. Drake, Appl. Environ. Microbiol. 69:1662-1669, 2003). This hypothesis implies that the denitrifiers in the earthworm gut are not endemic to the gut but rather are regular members of the soil denitrifier population. To test this hypothesis, the denitrifier populations of gut and soil from three different sites were comparatively assessed by sequence analysis of nosZ, the gene for the terminal enzyme in denitrification, N₂O reductase. A total of 182 and 180 nosZ sequences were retrieved from gut and soil, respectively; coverage of gene libraries was 79 to 100%. Many of the nosZ sequences were heretofore unknown, clustered with known soil-derived sequences, or were related to N₂O reductases of the genera Bradyrhizobium, Brucella, Dechloromonas, Flavobacterium, Pseudomonas, Ralstonia, and Sinorhizobium. Although the numbers of estimators for genotype richness of sequence data from the gut were higher than those of soil, only one gut-derived nosZ sequence did not group phylogenetically with any of the soil-derived nosZ sequences. Thus, the phylogenies of nosZ from gut and soil were not dissimilar, indicating that gut denitrifiers are soil derived.     

Similar neutralizing activity in the HIV-1 infected long term non-progressors(LTNPs) and typical progressors(TPs)

Neutralizing antibodies are considered to be an important protective parameter used in HIV-l vaccine evaluation.However,the exact role that neutralizing antibodies plays in controlling the disease prog...     

Platelet Specific Promoters Are Insufficient to Express Protease Activated Receptor 1 (PAR1) Transgene in Mouse Platelets

The in vivo study of protease activated receptors (PARs) in platelets is complicated due to species specific expression profiles. Human platelets express PAR1 and PAR4 whereas mouse platelets express PAR3 and PAR4. Further, PAR subtypes interact with one another to influence activation and signaling. The goal of the current study was to generate mice expressing PAR1 on their platelets using transgenic approaches to mimic PAR expression found in human platelets. This system would allow us to examine specific signaling from PAR1 and the PAR1-PAR4 heterodimer in vivo. Our first approach used the mouse GPIbα promoter to drive expression of mouse PAR1 in platelets (GPIbα-Tg-mPAR1). We obtained the expected frequency of founders carrying the transgene and had the expected Mendelian distribution of the transgene in multiple founders. However, we did not observe expression or a functional response of PAR1. As a second approach, we targeted human PAR1 with the same promoter (GPIbα-Tg-hPAR1). Once again we observed the expected frequency and distributing of the transgene. Human PAR1 expression was detected in platelets from the GPIbα-Tg-hPAR1 mice by flow cytometry, however, at a lower level than for human platelets. Despite a low level of PAR1 expression, platelets from the GPIbα-Tg-hPAR1 mice did not respond to the PAR1 agonist peptide (SFLLRN). In addition, they did not respond to thrombin when crossed to the PAR4^−/− mice. Finally, we used an alternative platelet specific promoter, human α_IIb, to express human PAR1 (α_IIb-Tg-hPAR1). Similar to our previous attempts, we obtained the expected number of founders but did not detect PAR1 expression or response in platelets from α_IIb-Tg-hPAR1 mice. Although unsuccessful, the experiments described in this report provide a resource for future efforts in generating mice expressing PAR1 on their platelets. We provide an experimental framework and offer considerations that will save time and research funds.     

Direct and Rapid Analysis of the Adhesion of Bacteria to Solid Surfaces: Interaction of Fluorescently Labeled Rhodococcus Strain GIN-1 (NCIMB 40340) Cells with Titanium-Rich Particles

A fluorimetric assay which enables direct and accurate analysis of the adhesion of bacteria to solid particles was developed. The assay is based on labeling of the bacteria with fluorescamine, which reacts with primary amino groups on the cell surface to yield a yellow fluorescence that is easily detectable by both fluorescence microscopy and spectrofluorimetry. As an example, fluorescent labeling of Rhodococcus strain GIN-1 (NCIMB 40340) cells enabled the detection and quantitative determination of their adsorption to TiO(inf2) and coal fly ash particles. Exposure of the cells to 10% acetone during the labeling reaction affected neither their viability nor their ability to adhere to these particles. Only a small fraction (^sim2%) of the total cell protein was labeled by fluorescamine upon staining of intact bacterial cells, which may indicate preferential labeling of certain proteins. Specificity studies carried out with the fluorescence assay confirmed previous findings that Rhodococcus strain GIN-1 cells possess high affinities for TiO(inf2), ZnO, and coal fly ash and low affinities for other metal oxides. In principle, the newly developed fluorimetric assay may be used for determination of cell adhesion to any solid matrix by either microscopic examination or epifluorescence measurements. In the present work, the adhesion of several other microorganisms to TiO(inf2) particles was tested as well, but their ability to adhere to these particles was significantly lower than that of Rhodococcus strain GIN-1 cells.     

Contribution of IL-1 beta and TNF-alpha to the initiation of the peripheral lung response to atmospheric particulates (PM10)

Alveolar macrophages (AM) play a key role in clearing atmospheric particulates from the lung surface and stimulating epithelial cells to produce proinflammatory mediators. The present study examines the role of "acute response" cytokines TNF-alpha and IL-1 beta released by AM exposed to ambient particulate matter with a diameter of <10 microm (PM(10)) in amplifying the proinflammatory mediator expression by A549 cells and human bronchial epithelial cells (HBEC). The results showed that supernatants from human AM incubated 24 h with PM(10) (100 microg/ml) contained more TNF-alpha, IL-1 beta, granulocyte-macrophage colony stimulating factor, IL-6, and IL-8 than nonexposed AM supernatants. The 3-h treatment of A549 cells with PM(10)-exposed AM supernatants increased TNF-alpha, IL-1 beta, IL-8, regulated on activation normal T-cells expressed and secreted (RANTES), and leukemia inhibitory factor mRNA compared with the treatment with nonexposed AM supernatants and, compared with untreated A549 cells, additionally increased ICAM-1 and monocyte chemotactic protein-1 mRNA. Preincubating PM(10)-exposed AM supernatants with anti-IL-1 beta antibodies reduced all the above mediators as well as VEGF mRNA expression (P < 0.05), while anti-TNF-alpha antibodies were less effective (P > 0.05), and the combination of the two antibodies most effective. When HBEC were treated similarly, anti-TNF-alpha antibodies had the greatest effect. In A549 cells PM(10)-exposed AM supernatants increased NF-kappa B, activator protein (AP)-1 and specificity protein 1 binding, while anti-TNF-alpha and anti-IL-1 beta antibodies reduced NF-kappa B and AP-1 binding. We conclude that AM-derived TNF-alpha and IL-1 beta provide a major stimulus for the production of proinflammatory mediators by lung epithelial cells and that their relative importance may depend on the type of epithelial cell target.