A-DNA accommodates adducts derived from diol epoxides of polycyclic aromatic hydrocarbons bound in a "side-stacking" mode

The minor groove of undistorted A-DNA provides a good binding site for planar, hydrophobic moieties such as unmetabolized polycyclic aromatic hydrocarbons (PAHs), and the base pairs at the ends of short oligodeoxynucleotide helices. It also accommodates the chief adduct derived from the metabolically activated form of the carcinogen benzo[a]pyrene. B-DNA lacks such a site. Computerized models have been generated for the major (N2-guanine-linked) adducts formed at this site by both + and - enantiomers of anti-benzo[a]pyrene-7,8-dihydrodiol-9,10-epoxide (anti-BPDE) with poly(dG).poly(dC) in the A-DNA conformation. The BPDE adducts lie in the shallow, relatively hydrophobic minor groove of the A-DNA after empirical potential energy minimization using the program AMBER. We term this binding mode "side-stacking." The side-stacked + anti-BPDE may constitute the chief carcinogenic lesion derived from benzo[a]pyrene.     

Degradation of Petroleum by an Alga, Prototheca Zopfii

Prototheca zopfii is an achlorophyllous alga which degrades oil. It has been found to degrade 10 and 40% of a motor oil and crude oil, respectively, when tested under appropriate conditions. Degradation of the crude oil observed in this study compares well with the amount of degradation accomplished by bacteria. P. zopfii was found to degrade a greater percentage of the aromatic hydrocarbons in motor oil than of the saturated hydrocarbons and a greater percentage of saturated hydrocarbons in crude oil than of aromatic hydrocarbons. Resins and asphaltens were produced during degradation of motor oil, whereas these fractions in crude oil were degraded. P. zopfii did not demonstrate preferential utilization of lower homologues of cycloalkanes and aromatics as has been observed with bacteria.     

Metabolism of alkylbenzenes, alkanes, and other hydrocarbons in anaerobic bacteria

Aromatic and aliphatic hydrocarbons are the main constituents of petroleum and its refined products. Whereas degradation of hydrocarbons by oxygen-respiring microorganisms has been known for about a century, utilization of hydrocarbons under anoxic conditions has been investigated only during the past decade. Diverse strains of anaerobic bacteria have been isolated that degrade toluene anaerobically, using nitrate, iron(III), or sulfate as electron acceptors. Also, other alkylbenzenes such as m-xylene or ethylbenzene are utilized by a number of strains. The capacity for anaerobic utilization of alkylbenzenes has been observed in members of the -, -, - and -subclasses of the Proteobacteria. Furthermore, denitrifying bacteria and sulfate-reducing bacteria with the capacity for anaerobic alkane degradation have been isolated, which are members of the - and -subclass, respectively. The mechanism of the activation of hydrocarbons as apolar molecules in the absence of oxygen is of particular interest.The biochemistry of anaerobic toluene degradation has been studied in detail. Toluene is activated by addition to fumarate to yield benzylsuccinate, which is then further metabolized via benzoyl-CoA. The toluene-activating enzyme presents a novel type of glycine radical protein. Another principle of anaerobic alkylbenzene activation has been observed in the anaerobic degradation of ethylbenzene. Ethylbenzene in denitrifying bacteria is dehydrogenated to 1-phenylethanol and further to acetophenone; the latter is also metabolized to benzoyl-CoA. Naphthalene is presumably activated under anoxic conditions by a carboxylation reaction. Investigations into the pathway of anaerobic alkane degradation are only at the beginning. The saturated hydrocarbons are mostlikely activated by addition of a carbon compound rather than by desaturation and hydration, as speculated about in some early studies. An anaerobic oxidation of methane with sulfate as electron acceptor has been documented in aquatic sediments. The process is assumed to involve a reversal of methanogenesis catalyzed by Archaea, and scavenge of an electron-carrying metabolite by sulfate-reducing bacteria. Among unsaturated non-aromatic hydrocarbons, anaerobic bacterial degradation has been demonstrated and investigated with n-alkenes, alkenoic terpenes and the alkyne, acetylene.     

Biodegradation of hydrocarbons by an extremely halophilic archaebacterium

An archaebacterium (strain EH4) able to biodegrade saturated and aromatic hydrocarbons has been isolated from a sail-marsh. Maximum growth on eicosane (62% of biodegradation, 10 h generation time) was reached in a medium prepared with a natural hypersaline water collected from a salt-marsh (3.5 mol/1 NaCl concentration). No growth on hydrocarbons was observed for NaCl concentration lower than 1.8 mol/1.     

Aerobic bacteria degrading both <Emphasis Type="Italic">n</Emphasis>-alkanes and aromatic hydrocarbons: an undervalued strategy for metabolic diversity and flexibility

Environmental pollution with petroleum toxic products has afflicted various ecosystems, causing devastating damage to natural habitats with serious economic implications. Some crude oil components may serve as growth substrates for microorganisms. A number of bacterial strains reveal metabolic capacities to biotransform various organic compounds. Some of the hydrocarbon degraders are highly biochemically specialized, while the others display a versatile metabolism and can utilize both saturated aliphatic and aromatic hydrocarbons. The extended catabolic profiles of the latter group have been subjected to systematic and complex studies relatively rarely thus far. Growing evidence shows that numerous bacteria produce broad biochemical activities towards different hydrocarbon types and such an enhanced metabolic potential can be found in many more species than the already well-known oil-degraders. These strains may play an important role in the removal of heterogeneous contamination. They are thus considered to be a promising solution in bioremediation applications. The main purpose of this article is to provide an overview of the current knowledge on aerobic bacteria involved in the mineralization or transformation of both n-alkanes and aromatic hydrocarbons. Variant scientific approaches enabling to evaluate these features on biochemical as well as genetic levels are presented. The distribution of multidegradative capabilities between bacterial taxa is systematically shown and the possibility of simultaneous transformation of complex hydrocarbon mixtures is discussed. Bioinformatic analysis of the currently available genetic data is employed to enable generation of phylogenetic relationships between environmental strain isolates belonging to the phyla Actinobacteria, Proteobacteria, and Firmicutes. The study proves that the co-occurrence of genes responsible for concomitant metabolic bioconversion reactions of structurally-diverse hydrocarbons is not unique among various systematic groups.     

Mutagenesis of the "leucine gate" to explore the basis of catalytic versatility in soluble methane monooxygenase

Soluble methane monooxygenase (sMMO) from methane-oxidizing bacteria is a multicomponent nonheme oxygenase that naturally oxidizes methane to methanol and can also cooxidize a wide range of adventitious substrates, including mono- and diaromatic hydrocarbons. Leucine 110, at the mouth of the active site in the alpha subunit of the hydroxylase component of sMMO, has been suggested to act as a gate to control the access of substrates to the active site. Previous crystallography of the wild-type sMMO has indicated at least two conformations of the enzyme that have the "leucine gate" open to different extents, and mutagenesis of homologous enzymes has indicated a role for this residue in the control of substrate range and regioselectivity with aromatic substrates. By further refinement of the system for homologous expression of sMMO that we developed previously, we have been able to prepare a range of site-directed mutations at position 110 in the alpha subunit of sMMO. All the mutants (with Gly, Cys, Arg, and Tyr, respectively, at this position) showed relaxations of regioselectivity compared to the wild type with monoaromatic substrates and biphenyl, including the appearance of new products arising from hydroxylation at the 2- and 3- positions on the benzene ring. Mutants with the larger Arg and Trp residues at position 110 also showed shifts in regioselectivity during naphthalene hydroxylation from the 2- to the 1- position. No evidence that mutagenesis of Leu 110 could allow very large substrates to enter the active site was found, however, since the mutants (like the wild type) were inactive toward the triaromatic hydrocarbons anthracene and phenanthrene. Thus, our results indicate that the "leucine gate" in sMMO is more important in controlling the precision of regioselectivity than the sizes of substrates that can enter the active site.     

Preliminary investigation of using volatile organic compounds from human expired air, blood and urine for locating entrapped people in earthquakes

A preliminary investigation on the possibility of using volatile organic compounds (VOCs) determination of expired air, blood and urine, for the early location of entrapped people in earthquakes, has been carried out. A group of 15 healthy subjects has been sampled. The identification of a common "core" of substances might provide indications of human presence that can be used for the development of a real time field analytical method for the on site detection of entrapped people. Expired air samples have been analyzed by thermal desorption GC/MS and VOCs from blood and urine by headspace SPME-GC/MS. Acetone was the only compound found common in all three matrices. Isoprene was found in both expired air and blood samples. Acetone and isoprene along with a number of saturated hydrocarbons were among the major constituents identified in expired air analysis. Various ketones (2-pentanone, 4-heptanone, 2-butanone) were also determined over urine specimens. Using the techniques and methods of field analytical chemistry and technology appears to be the proper approach for applying the results of the present study in real situations.     

Resolution of epoxide enantiomers of polycyclic aromatic hydrocarbons by chiral stationary-phase high-performance liquid chromatography

Enantiomers of nine K-region and one non-K-region epoxides of polycyclic aromatic hydrocarbons have been resolved by high-performance liquid chromatography with chiral stationary phases either ionically or covalently bonded to gamma-aminopropylsilanized silica. Resolution of enantiomers was confirmed by ultraviolet-visible absorption, circular dichroism, and mass spectral analyses. This method has been applied to the determination of optical purity and absolute configuration of the K-region epoxides formed in the metabolism of 1-methylbenz[a]anthracene, 7-methylbenz[a]anthracene, and 12-methylbenz[a]anthracene by rat liver microsomes.     

湖南湘潭地区空心莲子草叶甲自然种群的越冬虫态与越冬生境

卷蛾分索赤眼蜂Trichogrammatoidea bactrae Nagaraja和拟澳洲赤眼蜂Trichogramma confusum Viggiani是小菜蛾Plutella xylostella (L.)的优势寄生蜂。本研究利用“Y”型管测定了2种赤眼蜂对小菜蛾P. xylostella利他素-卵表和腹部鳞片13种饱和烷烃的嗅觉反应。结果显示: 卷蛾分索赤眼蜂交配雌蜂进入2, 6, 10, 14-四甲基十五烷、正十五烷、正十七烷处理区的百分数分别为80.65%, 68.75%和66.67%, 表明这3种烷烃对卷蛾分索赤眼蜂交配雌蜂有显著的吸引作用, 其他10种饱和烷烃对卷蛾分索赤眼蜂雌蜂无明显作用。拟澳洲赤眼蜂进入2, 6, 10, 14-四甲基十五烷、正三十五烷和正十五烷处理区的数目分别占84.38%, 70%和62.16%, 表明其对拟澳洲赤眼蜂交配雌蜂起着显著的吸引作用, 而另外10种烷烃对拟澳洲赤眼蜂雌蜂无作用。卷蛾分索赤眼蜂和拟澳洲赤眼蜂未交配雄蜂进入13种烷烃处理区和对照区的时间均无显著差异, 表明利他素各组分对2种赤眼蜂未交配雄蜂均无吸引作用。     

A consortium of immobilized rhodococci for oilfield wastewater treatment in a column bioreactor

The possible use of a consortium of actinobacteria from the genus Rhodococcus immobilized on a polymeric carrier has been investigated for oilfield wastewater treatment in a bioreactor. It has been found that Rhodococcus opacus IEGM 263 and Rhodococcus ruber IEGM 231 cells remain viable at high concentrations of mineral salts in water and are able to oxidize oil hydrocarbons up to 62–81%. It has been shown that the consortium of rhodococci was more efficient in the elimination of hydrocarbons from wastewater than monocultures.     

Oil degradation by basidiomycetes in soil and peat at low temperatures

A total of 17 basidiomycete strains causing white rot and growing on oil-contaminated substrates have been screened. Three strains with high (Steccherinum murashkinskyi), average (Trametes maxima), and low (Pleurotus ostreatus) capacities for the colonization of oil-contaminated substrates have been selected. The potential for degrading crude oil hydrocarbons has been assessed with the use of fungi grown on nonsterile soil and peat at low temperatures. Candida sp. and Rhodococcus sp. commercial strains have been used as reference organisms with oil-degrading ability. All microorganisms introduced in oil-contaminated soil have proved to be ineffective, whereas the inoculation of peat with basidiomycetes and oil-degrading microorganisms accelerated the destruction of oil hydrocarbons. The greatest degradation potential of oil-aliphatic hydrocarbons has been found in S. murashlinskyi. T. maxima turned out to be the most successful in degrading aromatic hydrocarbons. It has been suggested that aboriginal microflora contributes importantly to the effectiveness of oil-destructing microorganisms. T. maxima and S. murashkinskyi strains are promising for further study as oil-oxidizing agents during bioremediation of oil-contaminated peat soil under conditions of low temperatures.     

Characterization of Petroleum-Contaminated Soils by Thin-Layer Chromatography with Flame Ionization Detection

Petroleum hydrocarbons from 20 soils from refineries or other industrial sites were extracted with a mixture of chloroform and methanol (1:1, v/v), and the extracts were analyzed by thin layer chromatography with flame ionization detection (TLC/FID). The TLC/FID procedure has been used widely in biological and medical research but generally has been underutilized in environmental chemistry. The analysis method involved spotting a small volume of sample extract (typically 1 to 3?µl) on ten silica-coated quartz rods, and chromatographically separating constituents in the spots using solvent systems of increasing polarities (hexane, toluene, and dichloromethane + methanol). We achieved complete separation of saturated hydrocarbons, aromatic hydrocarbons, resins, and asphaltenes from the hydrocarbon-contaminated soils with this method. Analysis of the separated constituents by TLC/FID also allowed quantification of aromatic and aliphatic hydrocarbons without interference from soil biogenic lipids. A simplified version of the method permitted excellent separation of aliphatics +aromatics (forming a single peak) from resins and asphaltenes. The procedure is rapid (complete analysis of ten samples in about 1?h after extraction). Thus, the method seems well suited for synoptic surveys or screening and characterizing numerous samples prior to using more detailed and costly analyses.     

The reduction of wax precipitation in waxy crude oils by <Emphasis Type="Italic">Pseudomonas</Emphasis> species

Crude oil with different concentrations was subjected to Pseudomonas species at 37 degrees C and various incubation periods. The results showed that Pseudomonas species grew faster at 1% (v/v) concentration of crude oil and exhibited high biodegradation ability within 1 week. On measuring the emulsification activity and emulsion stability during different stages of growth, in various immiscible hydrocarbons, it appeared that the species was able to produce a stable emulsion with a maximum at the end of stationary phase of growth. The gas chromatography analysis of the saturated hydrocarbons of crude oil showed that, an increase in concentration of iso-alkanes in the range of C15-C20, and a bioconversion of heavy iso-alkanes in the range of C21-C22+. Chemical analysis of crude oil by liquid chromatographic technique before and after growth showed that, the saturated alkanes were more degradable than aromatic and asphaltenic compounds. Treatment by Pseudomonas species may possibly be an effective method for the biodegradation of heavy paraffinic hydrocarbon leading to an enhancement in crude oil properties.     

Synthesis of the enantiomers of some methyl-branched cuticular hydrocarbons of the ant, Diacamma sp.

The enantiomers of 3-methylpentacosane, 3-methylheptacosane, 3-methylnonacosane, 13-methylheptacosane, and 5-methylheptacosane were synthesized by starting from the enantiomers of 2-methylbutyl bromide or citronellol. These methyl-branched alkanes are the characteristic components of the cuticular hydrocarbons of queen of the ant, Diacamma sp..     

Degradation of fluorene and fluoranthene by the basidiomycete <Emphasis Type="Italic">Pleurotus ostreatus</Emphasis>

The dependence of the degree of fluorene and fluoranthene degradation by the fungus Pleurotus ostreatus D1 on the culture medium composition has been studied. Polycyclic aromatic hydrocarbons (PAHs) have been transformed in Kirk’s medium (under conditions of laccase production) with the formation of a quinone metabolite and 9-fluorenone upon the use of fluoranthene and fluorene as substrates, respectively. More complete degradation with the formation of an intermediate metabolite, phthalic acid that has undergone subsequent utilization, has occurred in basidiomycete-rich medium (under the production of both laccase and versatile peroxidase). The formation of phthalic acid as a metabolite of fluoranthene degradation by lignolytic fungi has been revealed for the first time. The data allow the supposition that both extracellular laccase and laccase on the mycelium surface can participate in the initial stages of PAH metabolism, while versatile peroxidase is necessary for the oxidation of the formed metabolites. A scheme of fluorene metabolism by Pleurotus ostreatus D1 is suggested.     

卷蛾分索赤眼蜂和拟澳洲赤眼蜂对小菜蛾利他素各成分的嗅觉反应

卷蛾分索赤眼蜂Trichogrammatoidea bactrae Nagaraja和拟澳洲赤眼蜂Trichogramma confusum Viggiani是小菜蛾Plutella xylostella (L.)的优势寄生蜂。本研究利用“Y”型管测定了2种赤眼蜂对小菜蛾P. xylostella利他素-卵表和腹部鳞片13种饱和烷烃的嗅觉反应。结果显示: 卷蛾分索赤眼蜂交配雌蜂进入2, 6, 10, 14-四甲基十五烷、正十五烷、正十七烷处理区的百分数分别为80.65%, 68.75%和66.67%, 表明这3种烷烃对卷蛾分索赤眼蜂交配雌蜂有显著的吸引作用, 其他10种饱和烷烃对卷蛾分索赤眼蜂雌蜂无明显作用。拟澳洲赤眼蜂进入2, 6, 10, 14-四甲基十五烷、正三十五烷和正十五烷处理区的数目分别占84.38%, 70%和62.16%, 表明其对拟澳洲赤眼蜂交配雌蜂起着显著的吸引作用, 而另外10种烷烃对拟澳洲赤眼蜂雌蜂无作用。卷蛾分索赤眼蜂和拟澳洲赤眼蜂未交配雄蜂进入13种烷烃处理区和对照区的时间均无显著差异, 表明利他素各组分对2种赤眼蜂未交配雄蜂均无吸引作用。     

Molecular characterization of the nonphotosynthetic partner bacterium in the consortium "Chlorochromatium aggregatum"

Phototrophic consortia represent valuable model systems for the study of signal transduction and coevolution between different bacteria. The phototrophic consortium "Chlorochromatium aggregatum" consists of a colorless central rod-shaped bacterium surrounded by about 20 green-pigmented epibionts. Although the epibiont was identified as a member of the green sulfur bacteria, and recently isolated and characterized in pure culture, the central colorless bacterium has been identified as a member of the beta-Proteobacteria but so far could not be characterized further. In the present study, "C. aggregatum" was enriched chemotactically, and the 16S rRNA gene sequence of the central bacterium was elucidated. Based on the sequence information, fluorescence in situ hybridization probes targeting four different regions of the 16S rRNA were designed and shown to hybridize exclusively to cells of the central bacterium. Phylogenetic analyses of the 1,437-bp-long sequence revealed that the central bacterium of "C. aggregatum" represents a so far isolated phylogenetic lineage related to Rhodoferax spp., Polaromonas vacuolata, and Variovorax paradoxus within the family Comamonadaceae. The majority of relatives of this lineage are not yet cultured and were found in low-temperature aquatic environments or aquatic environments containing xenobiotica or hydrocarbons. In CsCl-bisbenzimidazole equilibrium density gradients, genomic DNA of the central bacterium of "Chlorochromatium aggregatum" formed a distinct band which could be detected by quantitative PCR using specific primers. Using this method, the G+C content of the central bacterium was determined to be 55.6 mol%.     

Stereospecific synthesis of "para-hydroxymexiletine" and sodium channel blocking activity evaluation

Both enantiomers of "para-hydroxymexiletine" (PHM), one of the main metabolites of mexiletine, were synthesized and fully characterized. Properties of (R)- and (S)-PHM, in terms of blocking potency and stereoselectivity on frog skeletal muscle Na(+) channels, were evaluated. The presence of a hydroxy group on the aryloxy moiety in the 4-position, as in PHM, reduced potency with respect to mexiletine in reducing I(Na max). However, PHM showed clear use-dependent behavior similar to that of mexiletine and, in contrast with what is observed with the parent compound, maintained its stereoselectivity during the use-dependent block. Chirality 16:72-78, 2004.     

Fluorous "racemic" mixture synthesis: polysaccharide-based chiral columns for simultaneous demix and enantioseparation of racemic fluorous tagged compounds

The proof of concept experiments of fluorous "racemic" mixture synthesis (FRMS) is shown using polysaccharide-based chiral stationary phases. The mixture of racemic O-benzoylmandelate derivatives bearing different lengths of fluorous cleavable tags undergoes sequential reactions to provide individual derivatives as well as their enantiomers resolved on polysaccharide-based chiral HPLC columns (DAICEL CHIRALCEL and CHIRALPAK series).     

Hydrocarbon and multibranched ester waxes from the uropygial gland secretion of grebes (Podicipediformes).

The uropygial gland secretion of some grebes (Podicipediformes) had been shown to contain saturated and unsaturated aliphatic hydrocarbons and monoester waxes. While ester waxes are common constituents of preen gland secretions, nonisoprenoid hydrocarbons have not been detected hitherto. The wax constituents are very complex, belonging to several multibranched homologous series, including unusual acids with ethyl branches. The waxes were identified by gas-liquid chromatography-mass spectrometry and equivalent chain length comparisons. A method for the prediction of equivalent chain length values of unknown methyl esters is offered. The results are discussed from a chemotaxonomic viewpoint.