Biomedical subjects

D W Westlake

Publications and source records attributed to D W Westlake.

At least 19 recordsLinked to original sources

PubMed1998

Comparison of oil composition changes due to biodegradation and physical weathering in different oils.

The well-characterized Alberta Sweet Mixed Blend oil and several other oils which are commonly transported in Canada were physically weathered and then incubated with a defined microbial inoculum. The purpose was to produce quantitative data on oil components and component groups which are more susceptible or resistant to biodegradation, and to determine how oils rank in relation to each other in terms of biodegradation potential. The biodegraded oils were characterized by quantitative determination of changes in important hydrocarbon groups including the total petroleum hydrocarbons, total saturates and aromatics, and also by quantitation of more than 100 individual target aliphatic, aromatic and biomarker components. The study reveals a pattern of distinct oil composition changes due to biodegradation, which is significantly different from the pattern due to physical or short-term weathering. It is important to be able to distinguish between these two forms of loss, so that loss due to weathering is not interpreted as loss due to biodegradation in the laboratory or in the field. Based on these findings, the oil composition changes due to biodegradation can be readily differentiated from those due to physical weathering. To rank the tested oils with respect to biodegradability, losses in total petroleum hydrocarbons and aromatics were used to calculate biodegradation potential indices, employing equations proposed by Environment Canada and the US National Oceanic and Atmospheric Administration. The different methods produced very similar biodegradation trends, confirming that patterns of oil biodegradability do exist.

Bacteria↗

PubMed1996

Transposon and spontaneous deletion mutants of plasmid-borne genes encoding polycyclic aromatic hydrocarbon degradation by a strain of Pseudomonas fluorescens.

Pseudomonas fluorescens strain LP6a, isolated from petroleum condensate-contaminated soil, utilizes the polycyclic aromatic hydrocarbons (PAHs) naphthalene, phenanthrene, anthracene and 2-methylnaphthalene as sole carbon and energy sources. The isolate also co-metabolically transforms a suite of PAHs and heterocycles including fluorene, biphenyl, acenaphthene, 1-methylnaphthalene, indole, benzothiophene, dibenzothiophene and dibenzofuran, producing a variety of oxidized metabolites. A 63 kb plasmid (pLP6a) carries genes encoding enzymes necessary for the PAH-degrading phenotype of P. fluorescens LP6a. This plasmid hybridizes to the classical naphthalene degradative plasmids NAH7 and pWW60, but has different restriction endonuclease patterns. In contrast, plasmid pLP6a failed to hybridize to plasmids isolated from several phenanthrene-utilizing strains which cannot utilize naphthalene. Plasmid pLP6a exhibits reproducible spontaneous deletions of a 38 kb region containing the degradative genes. Two gene clusters corresponding to the archetypal naphthalene degradation upper and lower pathway operons, separated by a cryptic region of 18 kb, were defined by transposon mutagenesis. Gas chromatographic-mass spectrometric analysis of metabolites accumulated by selected transposon mutants indicates that the degradative enzymes encoded by genes on pLP6a have a broad specificity permitting the oxidation of a suite of polycyclic aromatic and heterocyclic substrates.

Biodegradation, Environmental↗

PubMed1996

Environmental gasoline-utilizing isolates and clinical isolates of Pseudomonas aeruginosa are taxonomically indistinguishable by chemotaxonomic and molecular techniques.

A total of 42 Pseudomonas aeruginosa strains was isolated previously from clinical sources (27 strains) and from a gasoline-contaminated aquifer (15 strains). Selected strains were subjected to taxonomic tests involving chemical and molecular biological techniques, including membrane fatty acid analysis, phage-sensitivity, growth temperature range, presence of plasmids, and PCR-amplification and sequencing of a species-specific 16S-23S rDNA internal transcribed spacer region. The clinical and environmental isolates formed a coherent taxonomic group with few distinguishing characteristics. Of the phenotypes observed, a consistent difference was the ability of the aquifer strains to utilize gasoline supplied in the gas phase as sole carbon source and, conversely, the inability of the clinical strains to do so. Fourteen of the 15 environmental strains possessed similar-sized cryptic plasmids. The clinical isolates either lacked detectable plasmids or contained plasmids of a different size. The observation that the clinical and environmental isolates of P. aeruginosa were taxonomically indistinguishable is discussed in terms of its relevance to environmental-regulatory guidelines because P. aeruginosa, a known opportunistic pathogen, is a prime candidate for use in bioremediation processes involving deliberate release of this organism to the environment.

Bacteriophages↗

PubMed1994

Lignin peroxidase oxidation of aromatic compounds in systems containing organic solvents.

Lignin peroxidase from Phanerochaete chrysosporium was used to study the oxidation of aromatic compounds, including polycyclic aromatic hydrocarbons and heterocyclic compounds, that are models of moieties of asphaltene molecules. The oxidations were done in systems containing water-miscible organic solvents, including methanol, isopropanol, N, N-dimethylformamide, acetonitrile, and tetrahydrofuran. Of the 20 aromatic compounds tested, 9 were oxidized by lignin peroxidase in the presence of hydrogen peroxide. These included anthracene, 1-, 2-, and 9-methylanthracenes, acenaphthene, fluoranthene, pyrene, carbazole, and dibenzothiophene. Of the compounds studied, lignin peroxidase was able to oxidize those with ionization potentials of <8 eV (measured by electron impact). The reaction products contain hydroxyl and keto groups. In one case, carbon-carbon bond cleavage, yielding anthraquinone from 9-methylanthracene, was detected. Kinetic constants and stability characteristics of lignin peroxidase were determined by using pyrene as the substrate in systems containing different amounts of organic solvent. Benzyl alkylation of lignin peroxidase improved its activity in a system containing water-miscible organic solvent but did not increase its resistance to inactivation at high solvent concentrations.

Journal Article↗

PubMed1994

Characterization of the diversity of sulfate-reducing bacteria in soil and mining waste water environments by nucleic acid hybridization techniques.

Nucleic acid hybridization techniques were used to characterize the sulfate-reducing bacterial communities at seven waste water and two soil sites in Canada. Genomic DNA was obtained from liquid enrichment cultures of samples taken from these nine sites. The liquid enrichment protocol favored growth of the sulfate-reducing bacterial component of the communities at these sites. The genomic DNA preparations were analyzed with (i) a specific gene probe aimed at a single genus (Desulfovibrio), (ii) a general 16S rRNA gene probe aimed at all genera of sulfate-reducing bacteria and other bacteria, and (iii) whole genome probes aimed at specific bacteria. This three-pronged approach provided information on the sulfate-reducing bacterial community structures for the nine sites. These were compared with each other and with the sulfate-reducing bacterial communities of western Canadian oil field production waters, studied previously. It was found that there is considerable diversity in the sulfate-reducing bacterial community at each site. Most sulfate-reducing bacteria isolated from distinct sites are genomically different and differ also from sulfate-reducing bacteria found in oil field production waters.

Bacteria↗

PubMed1993

Effect of water-miscible organic solvents on the catalytic activity of cytochrome c.

The effect of five water-miscible organic solvents (tetrahydrofuran, N,N-dimethylformamide, acetonitrile, 2-propanol, and methanol) on the oxidation of pinacyanol chloride (Quinaldine Blue) by horse heart cytochrome c was determined. Hydrogen peroxide was used as the oxidant, and a change in catalytic property of the dissolved protein was observed after a certain threshold concentration of the organic solvent had been reached. The maximum specific activity was correlated with the Dimroth-Reichardt parameter for the solvents, which is directly related to the free energy of the solvation process. The kinetic constants for the oxidation of pinacyanol chloride were determined in systems containing different proportions of tetrahydrofuran. The best catalytic efficiency (kcat/KM,app) was obtained in a system containing 50% tetrahydrofuran in phosphate buffer. In a mixture containing 90% tetrahydrofuran, cytochrome c showed 18% of its maximum activity. The inactivation of cytochrome c was mainly due to the presence of hydrogen peroxide, and a direct correlation was found between the inactivation constant and the concentration of hydrogen peroxide in the system. The chemical modifications and immobilization of cytochrome c were able to change its biocatalytic activity and stability in the organic solvent system. The kinetic constants and the inactivation of three other type c cytochromes, from Saccharomyces cerevisiae, Pseudomonas aeruginosa, and Desulfovibrio vulgaris Hildenborough in a system containing 90% tetrahydrofuran were compared with those of cytochrome c from horse heart. Cytochrome c551 from P. aeruginosa showed the best stability against hydrogen peroxide and a higher catalytic efficiency than that of horse heart cytochrome c.

Animals↗

PubMed1993

Quantitative reverse sample genome probing of microbial communities and its application to oil field production waters.

This paper presents a protocol for quantitative analysis of microbial communities by reverse sample genome probing is presented in which (i) whole community DNA is isolated and labeled in the presence of a known amount of an added internal standard and (ii) the resulting spiked reverse genome probe is hybridized with a master filter on which denatured genomic DNAs from bacterial standards isolated from the target environment were spotted in large amounts (up to 1,500 ng) in order to improve detection sensitivity. This protocol allowed reproducible fingerprinting of the microbial community in oil field production waters at 19 sites from which water and biofilm samples were collected. It appeared that selected sulfate-reducing bacteria were significantly enhanced in biofilms covering the metal surfaces in contact with the production waters.

Journal Article↗

PubMed1992

Identification of distinct communities of sulfate-reducing bacteria in oil fields by reverse sample genome probing.

Thirty-five different standards of sulfate-reducing bacteria, identified by reverse sample genome probing and defined as bacteria with genomes showing little or no cross-hybridization, were in part characterized by Southern blotting, using 16S rRNA and hydrogenase gene probes. Samples from 56 sites in seven different western Canadian oil field locations were collected and enriched for sulfate-reducing bacteria by using different liquid media containing one of the following carbon sources: lactate, ethanol, benzoate, decanoate, propionate, or acetate. DNA was isolated from the enrichments and probed by reverse sample genome probing using master filters containing denatured chromosomal DNAs from the 35 sulfate-reducing bacterial standards. Statistical analysis of the microbial compositions at 44 of the 56 sites indicated the presence of two distinct communities of sulfate-reducing bacteria. The discriminating factor between the two communities was the salt concentration of the production waters, which were either fresh water or saline. Of 34 standards detected, 10 were unique to the fresh water and 18 were unique to the saline oil field environment, while only 6 organisms were cultured from both communities.

Journal Article↗

PubMed1991

Reverse sample genome probing, a new technique for identification of bacteria in environmental samples by DNA hybridization, and its application to the identification of sulfate-reducing bacteria in oil field samples.

A novel method for the identification of bacteria in environmental samples by DNA hybridization is presented. It is based on the fact that, even within a genus, the genomes of different bacteria may have little overall sequence homology. This allows the use of the labeled genomic DNA of a given bacterium (referred to as a "standard") to probe for its presence and that of bacteria with highly homologous genomes in total DNA obtained from an environmental sample. Alternatively, total DNA extracted from the sample can be labeled and used to probe filters on which denatured chromosomal DNA from relevant bacterial standards has been spotted. The latter technique is referred to as reverse sample genome probing, since it is the reverse of the usual practice of deriving probes from reference bacteria for analyzing a DNA sample. Reverse sample genome probing allows identification of bacteria in a sample in a single step once a master filter with suitable standards has been developed. Application of reverse sample genome probing to the identification of sulfate-reducing bacteria in 31 samples obtained primarily from oil fields in the province of Alberta has indicated that there are at least 20 genotypically different sulfate-reducing bacteria in these samples.

Journal Article↗

PubMed1990

Production of Streptomyces clavuligerus isopenicillin N synthase in Escherichia coli using two-cistron expression systems.

Streptomyces clavuligerus isopenicillin N synthase (IPNS) gene expression was achieved in Escherichia coli by the construction of two-cistron expression systems formed in the high copy number plasmid vector pUC119. These two-cistron constructions were composed of the IPNS gene and its flanking sequences which encoded an upstream open reading frame (ORF), the IPNS ribosome binding site and a putative transcription terminator. No E. coli- like Streptomyces promoter motif was present upstream of the IPNS gene therefore transcriptional regulation of the two-cistron system was provided by the lac promoter of pUC119. Enzymatically active IPNS was detected in E. coli cells harboring the recombinant plasmids thereby providing evidence for the activity of the IPNS ORF and for the feasibility of production of S. clavuligerus IPNS in E. coli. These results indicate that simple two-cistron constructions involving foreign gene flanking sequences may be used to express foreign proteins in E. coli.

Base Sequence↗

PubMed1990

Oxygen derepresses deacetoxycephalosporin C synthase and increases the conversion of penicillin N to cephamycin C in Streptomyces clavuligerus.

When dissolved oxygen (DO) was maintained at saturation level during batch fermentations of Streptomyces clavuligerus (NRRL 3585), the accumulation of the intermediate penicillin N was lowered while formation of the end product cephamycin C was increased relative to fermentations without DO control. The specific activity of the penicillin ring-expansion enzyme deacetoxycephalosporin C synthase (DAOCS) was increased 2.3-fold under oxygen saturated conditions, whereas the penicillin ring-cyclizing enzyme isopenicillin N synthase (IPNS) showed only a 1.3-fold increase. Thus oxygen derepression of DAOCS appears to be an important regulatory mechanism in the conversion of penicillin N to cephamycin C in S. clavuligerus. IPNS, an early acting enzyme in cephamycin C biosynthesis, and DAOCS, which acts late in the pathway, both disappeared from cell extracts at 60 h, just prior to cessation of cephamycin production.

Cephamycins↗

PubMed1990

Distribution of Hydrogenase Genes in Desulfovibrio spp. and Their Use in Identification of Species from the Oil Field Environment.

The distribution of genes for [Fe], [NiFe], and [NiFeSe] hydrogenases was determined for 22 Desulfovibrio species. The genes for [NiFe] hydrogenase were present in all species, whereas those for the [Fe] and [NiFeSe] hydrogenases had a more limited distribution. Sulfate-reducing bacteria from 16S rRNA groups other than the genus Desulfovibrio (R. Devereux, M. Delaney, F. Widdel, and D. A. Stahl, J. Bacteriol. 171:6689-6695, 1989) did not react with the [NiFe] hydrogenase gene probe, which could be used to identify different Desulfovibrio species in oil field samples following growth on lactate-sulfate medium.

Journal Article↗

PubMed1990

Purification and partial characterization of delta-(L-alpha-aminoadipyl)-L-cysteinyl-D-valine synthetase from Streptomyces clavuligerus.

delta-(L-alpha-Aminoadipyl)-L-cysteinyl-D-valine synthetase (ACVS) was purified from Streptomyces clavuligerus by a combination of salt precipitation, ultrafiltration, and anion-exchange chromatography. The final purified material gave two protein bands with molecular weights of 283,000 and 32,000 by sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Electrophoresis in nondenaturing gels gave a single protein band with an estimated molecular weight of 560,000. These results suggest that ACVS is a multimer composed of nonidentical subunits.

Chromatography↗

PubMed1990

Mineralization of [14C]hexadecane and [14C]phenanthrene in crude oil: specificity among bacterial isolates.

Bacteria isolated from freshwater, marine, and estuarine samples were tested for the ability to produce 14CO2 from n-[1-14C]hexadecane or [9-14C]phenanthrene added to Prudhoe Bay crude oil. Of 138 isolates tested, 54 (39%) mineralized the model aliphatic compound hexadecane and 6 (4%) mineralized the model aromatic compound phenanthrene. None mineralized both compounds. There was no apparent correlation between degradative ability and genus or source. Additional hydrocarbon-degrading bacteria from diverse sources were tested and found to mineralize either hexadecane or phenanthrene. Of 61 hexadecane- and 21 phenanthrene-mineralizing bacteria tested, none mineralized both model compounds. Selected isolates and commercially available cultures were tested for mineralization of specific 14C-labelled mono-, di-, and tri-cyclic aromatics. An apparent hierarchy of degradation was observed: strains mineralizing the mono- and di-cyclic aromatics toluene and naphthalene did not mineralize biphenyl or the tricyclic aromatics anthracene and phenanthrene, whereas those strains that mineralized the tricyclic aromatics also mineralized the smaller substrates. Similarly, not all n-alkane-mineralizing isolates tested mineralized the isoprenoid pristane. A combined culture consisting of one aliphatic- and one aromatic-degrading isolate was tested for mineralization of the model compounds and for degradation of other crude oil components by gas chromatography. No synergism or antagonism was observed compared with degradation by the individual isolates.

Alkanes↗

PubMed1990

Expression of dibenzothiophene-degradative genes in two Pseudomonas species.

The genes encoding dibenzothiophene (DBT) degradation in Pseudomonas alcaligenes strain DBT2 were cloned into plasmid pC1 by other workers. This plasmid was conjugally transferred into a spontaneous variant of Pseudomonas sp. HL7b (designated HL7bR) incapable of oxidizing DBT (Dbt- phenotype). Acquisition of plasmid pC1 simultaneously restored oxidation of DBT and naphthalene to the transconjugant, although the primary DBT metabolite produced by transconjugant HL7bR(pC1) corresponded to that produced by wild-type strain DBT2 rather than that from wild-type strain HL7b. Inducers of the naphthalene pathway (naphthalene, salicylic acid, and 2-aminobenzoate) stimulated DBT oxidation in transconjugant HL7bR(pC1) when present at 0.1 mM concentrations but had no effect on wild-type strain HL7b. Higher concentrations (5 mM) of salicylic acid and naphthalene were inhibitory to DBT oxidation in all strains. DNA-DNA hybridization was not observed between plasmid pC1 and genomic DNA from strains HL7b or HL7bR, nor between authentic naphthalene-degradative genes (plasmid NAH2) and either plasmid pC1 or strain HL7b, despite the observation that the degradative genes encoded on plasmid pC1 functionally resembled broad-specificity naphthalene-degradative genes. Transconjugant HL7bR(pC1) is a mosaic of the parental types regarding DBT metabolite production, regulation, and use of carbon sources.

Biodegradation, Environmental↗

PubMed1989

Effect of emulsan on biodegradation of crude oil by pure and mixed bacterial cultures.

Crude oil was treated with purified emulsan, the heteropolysaccharide bioemulsifier produced by Acinetobacter calcoaceticus RAG-1. A mixed bacterial population as well as nine different pure cultures isolated from various sources was tested for biodegradation of emulsan-treated and untreated crude oil. Biodegradation was measured both quantitatively and qualitatively. Recovery of CO(2) from mineralized C-labeled substrates yielded quantitative data on degradation of specific compounds, and capillary gas chromatography of residual unlabeled oil yielded qualitative data on a broad spectrum of crude oil components. Biodegradation of linear alkanes and other saturated hydrocarbons, both by pure cultures and by the mixed population, was reduced some 50 to 90% after emulsan pretreatment. In addition, degradation of aromatic compounds by the mixed population was reduced some 90% in emulsan-treated oil. In sharp contrast, aromatic biodegradation by pure cultures was either unaffected or slightly stimulated by emulsification of the oil.

Journal Article↗

PubMed1989

Isopenicillin N synthase and desacetoxycephalosporin C synthase activities during defined medium fermentations of Streptomyces clavuligerus: effect of oxygen and iron supplements.

When the level of dissolved oxygen was increased to saturation in defined media fermentations of Streptomyces clavuligerus, the total duration of activity of the penicillin ring cyclization enzyme, isopenicillin N synthase (IPNS), was extended by at least 20 h; however, no increase in the stability of the ring expansion enzyme, desacetoxycephalosporin C synthase (DAOCS), was observed. Consequently, the conversion of the excreted intermediate penicillin N to cephamycin C was 15-20% less efficient at this high oxygen concentration. The increased dissolved oxygen level also led to the complete loss of IPNS and DAOCS activities for 4 h during the period of fastest growth, and the rate of specific cephamycin C production fell to zero. A several hundred fold increase in the level of iron in the defined media resulted in a sixfold improvement in the rate of specific cephamycin C production after 60 h fermentation. This increased rate appeared to be due to an elevation in the in vivo activities of a number of the cephamycin biosynthetic enzymes, particularly those catalysing later pathway steps.

Cephamycins↗

PubMed1988

Cloning and nucleotide sequence determination of the isopenicillin N synthetase gene from Streptomyces clavuligerus.

The isopenicillin N synthetase (IPNS) gene from Streptomyces clavuligerus was isolated from an Escherichia coli plasmid library of S. clavuligerus genomic DNA fragments using a 44-mer mixed oligodeoxynucleotide probe. The nucleotide sequence of a 3-kb region of the cloned fragment from the plasmid, pBL1, was determined and analysis of the sequence showed an open reading frame that could encode a protein of 329 amino acids with an Mr of 36,917. When the S. clavuligerus DNA from pBL1 was introduced into an IPNS-deficient mutant of S. clavuligerus on the Streptomyces vector pIJ941, the recombinant plasmid was able to complement the mutation and restore IPNS activity. The protein coding region of the S. clavuligerus IPNS gene shows about 63% and 62% similarity to the Cephalosporium acremonium and Penicillium chrysogenum IPNS nucleotide sequences, respectively, and the predicted amino acid sequence of the encoded protein showed about 56% similarity to both fungal sequences.

Acremonium↗