Linking microbial oxidation of arsenic with detection and phylogenetic analysis of arsenite oxidase genes in diverse geothermal environments.

The identification and characterization of genes involved in the microbial oxidation of arsenite will contribute to our understanding of factors controlling As cycling in natural systems. Towards this goal, we recently characterized the widespread occurrence of aerobic arsenite oxidase genes (aroA-like) from pure-culture bacterial isolates, soils, sediments and geothermal mats, but were unable to detect these genes in all geothermal systems where we have observed microbial arsenite oxidation. Consequently, the objectives of the current study were to measure arsenite-oxidation rates in geochemically diverse thermal habitats in Yellowstone National Park (YNP) ranging in pH from 2.6 to 8, and to identify corresponding 16S rRNA and aroA genotypes associated with these arsenite-oxidizing environments. Geochemical analyses, including measurement of arsenite-oxidation rates within geothermal outflow channels, were combined with 16S rRNA gene and aroA functional gene analysis using newly designed primers to capture previously undescribed aroA-like arsenite oxidase gene diversity. The majority of bacterial 16S rRNA gene sequences found in acidic (pH 2.6-3.6) Fe-oxyhydroxide microbial mats were closely related to Hydrogenobaculum spp. (members of the bacterial order Aquificales), while the predominant sequences from near-neutral (pH 6.2-8) springs were affiliated with other Aquificales including Sulfurihydrogenibium spp., Thermocrinis spp. and Hydrogenobacter spp., as well as members of the Deinococci, Thermodesulfobacteria and beta-Proteobacteria. Modified primers designed around previously characterized and newly identified aroA-like genes successfully amplified new lineages of aroA-like genes associated with members of the Aquificales across all geothermal systems examined. The expression of Aquificales aroA-like genes was also confirmed in situ, and the resultant cDNA sequences were consistent with aroA genotypes identified in the same environments. The aroA sequences identified in the current study expand the phylogenetic distribution of known Mo-pterin arsenite oxidase genes, and suggest the importance of three prominent genera of the order Aquificales in arsenite oxidation across geochemically distinct geothermal habitats ranging in pH from 2.6 to 8.

Complete and draft genome sequences of six members of the Aquificales.

The Aquificales are widespread in marine and terrestrial hydrothermal environments. Here, we report the complete and draft genome sequences of six new members of the Aquificales: two marine species, Persephonella marina strain EX-H1 and Hydrogenivirga strain 128-5-R1 (from the East Pacific Rise, 9 degrees 50.3'N, 104 degrees 17.5'W, and the Eastern Lau Spreading Center, 176 degrees 11.5'W, 20 degrees 45.8'S, respectively), and four terrestrial isolates, Sulfurihydrogenibium azorense strain Az-Fu1, Sulfurihydrogenibium yellowstonense strain SS-5, and Sulfurihydrogenibium strain Y03AOP1 (from Furnas, Azores, Portugal, and Calcite Springs and Obsidian Pool in Yellowstone National Park, United States, respectively), and the only thermoacidophilic isolate, Hydrogenobaculum strain Y04AAS1 (from a stream adjacent to Obsidian Pool). Significant differences among the different species exist that include nitrogen metabolism, hydrogen utilization, chemotaxis, and signal transduction, providing insights into their ecological niche adaptations.

Two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8.

Alkane monooxygenases in Nocardioides sp. strain CF8 were examined at the physiological and genetic levels. Strain CF8 can utilize alkanes ranging in chain length from C(2) to C(16). Butane degradation by butane-grown cells was strongly inhibited by allylthiourea, a copper-selective chelator, while hexane-, octane-, and decane-grown cells showed detectable butane degradation activity in the presence of allylthiourea. Growth on butane and hexane was strongly inhibited by 1-hexyne, while 1-hexyne did not affect growth on octane or decane. A specific 30-kDa acetylene-binding polypeptide was observed for butane-, hexane-, octane-, and decane-grown cells but was absent from cells grown with octane or decane in the presence of 1-hexyne. These results suggest the presence of two monooxygenases in strain CF8. Degenerate primers designed for PCR amplification of genes related to the binuclear-iron-containing alkane hydroxylase from Pseudomonas oleovorans were used to clone a related gene from strain CF8. Reverse transcription-PCR and Northern blot analysis showed that this gene encoding a binuclear-iron-containing alkane hydroxylase was expressed in cells grown on alkanes above C(6). These results indicate the presence of two distinct monooxygenases for alkane oxidation in Nocardioides sp. strain CF8.

Isolation and characterization of alkane-utilizing Nocardioides sp. strain CF8.

A butane-utilizing bacterial strain CF8 was isolated and identified as a member of the genus Nocardioides from chemotaxonomic and 16S rDNA sequence analysis. Strain CF8 grew on alkanes ranging from C(2) to C(16) in addition to butane and various other substrates including primary alcohols, carboxylic acids, and phenol. Butane degradation by strain CF8 was inactivated by light, a specific inactivator of copper-containing monooxygenases. The unique thermal aggregation phenomenon of acetylene-binding polypeptides was also observed for strain CF8. These results suggest that butane monooxygenase in strain CF8 is a third example of the copper-containing monooxygenases previously described in ammonia oxidizers and methanotrophs.

Diversity in butane monooxygenases among butane-grown bacteria.

Butane monooxygenases of butane-grown Pseudomonas butanovora, Mycobacterium vaccae JOB5, and an environmental isolate, CF8, were compared at the physiological level. The presence of butane monooxygenases in these bacteria was indicated by the following results. (i) O(2) was required for butane degradation. (ii) 1-Butanol was produced during butane degradation. (iii) Acetylene inhibited both butane oxidation and 1-butanol production. The responses to the known monooxygenase inactivator, ethylene, and inhibitor, allyl thiourea (ATU), discriminated butane degradation among the three bacteria. Ethylene irreversibly inactivated butane oxidation by P. butanovora but not by M. vaccae or CF8. In contrast, butane oxidation by only CF8 was strongly inhibited by ATU. In all three strains of butane-grown bacteria, specific polypeptides were labeled in the presence of [(14)C]acetylene. The [(14)C]acetylene labeling patterns were different among the three bacteria. Exposure of lactate-grown CF8 and P. butanovora and glucose-grown M. vaccae to butane induced butane oxidation activity as well as the specific acetylene-binding polypeptides. Ammonia was oxidized by all three bacteria. P. butanovora oxidized ammonia to hydroxylamine, while CF8 and M. vaccae produced nitrite. All three bacteria oxidized ethylene to ethylene oxide. Methane oxidation was not detected by any of the bacteria. The results indicate the presence of three distinct butane monooxygenases in butane-grown P. butanovora, M. vaccae, and CF8.

Chloroform Cometabolism by Butane-Grown CF8, Pseudomonas butanovora, and Mycobacterium vaccae JOB5 and Methane-Grown Methylosinus trichosporium OB3b.

Chloroform (CF) degradation by a butane-grown enrichment culture, CF8, was compared to that by butane-grown Pseudomonas butanovora and Mycobacterium vaccae JOB5 and to that by a known CF degrader, Methylosinus trichosporium OB3b. All three butane-grown bacteria were able to degrade CF at rates comparable to that of M. trichosporium. CF degradation by all four bacteria required O(inf2). Butane inhibited CF degradation by the butane-grown bacteria, suggesting that butane monooxygenase is responsible for CF degradation. P. butanovora required exogenous reductant to degrade CF, while CF8 and M. vaccae utilized endogenous reductants. Prolonged incubation with CF resulted in decreased CF degradation. CF8 and P. butanovora were more sensitive to CF than either M. trichosporium or M. vaccae. CF degradation by all three butane-grown bacteria was inactivated by acetylene, which is a mechanism-based inhibitor for several monooxygenases. Butane protected all three butane-grown bacteria from inactivation by acetylene, which indicates that the same monooxygenase is responsible for both CF and butane oxidation. CF8 and P. butanovora were able to degrade other chlorinated hydrocarbons, including trichloroethylene, 1,2-cis-dichloroethylene, and vinyl chloride. In addition, CF8 degraded 1,1,2-trichloroethane. The results indicate the potential of butane-grown bacteria for chlorinated hydrocarbon transformation.

[Proliferating cell nuclear antigen (PCNA) immunolocalization in human nasal epithelium with chronic sinusitis detected by confocal laser scanning microscopy].

This study examines the immunohistological localization of proliferating cell nuclear antigen in the nasal and paranasal sinus epithelium from a group of patients undergoing sinus surgery for chronic sinusitis. PCNA immunoreactivity as determined by fluorescence intensity and the density of labeled cells as assessed by confocal laser scanning microscopy. The control group consisted of seven specimens taken from patients with post operative maxillary cyst and optic nerve canal fracture. In this group, most of the labeled cells were located on the basal cell layers with a few on the intermediate cell layers. The average labeled cell densities were 57.3 cells/mm2 on the basal cell layers and 15.9 cells/mm2 on the intermediate cell layer. The sinusitis group consisted of eleven patients. In contrast with the control group, the sinusitis epithelium displayed a significantly high proportion of goblet and intermediate cells positively stained for PCNA. The average densities were 84.9 cells/mm2 on the basal cell layers and 133.1 cells/mm2 on the intermediate cell layers in this group, the latter being nearly ten fold greater than that in the control group. Epithelial PCNA expression was correlated with the degree of inflammatory cell infiltration assessed by serial sections for each sample. A positive correlation was observed between these two factors (R = 0.63, Pearson). We believe that epithelial cell turnover is accelerated in chronic rhinosinusitis due to continuous exposure to various pathogens and host immune interventions. In those cases, goblet and intermediate cells would play the major role in enhanced epithelial proliferation.

Expression of proliferating cell nuclear antigen in cultured middle ear epithelial cells of the guinea pig.

Primary cultures of middle ear epithelium from the guinea pig were successfully established on type I collagen coated dishes. To characterize cellular outgrowth, antibodies to the proliferating cell nuclear antigen were used as a marker for spreading cells in the S phase of the cell cycle. A number of migrating epithelial cells positively stained for proliferating cell nuclear antigen after 7 and 14 days in culture. Confocal laser scanning microscopy was used to evaluate the localization pattern of this antigen, and the fluorescence intensity was quantified in different areas of the migrating epithelial sheet after various times in culture. Two distinct areas proved to be major sites of proliferating cell nuclear antigen expression. One was at the edge of the tissue explants from which multilayered epithelial cells had begun to migrate. The other was along the margin of the outgrowth, where the cells often had elongated shapes and were aligned in rows. The cells in both areas were identified as nonciliated cells; ciliated cells in the outgrowth showed little staining. We hypothesized that the outgrowth cells in this experiment might be identical to the migrating cells usually observed in renewing epithelia after injury. This model may provide a simple and reproducible method of evaluating the regenerative ability of the middle ear epithelium.

[A study of standardization of surveillance data 1). Significance of "corrected value of patients" and its application to exanthema subtium and erythema infectiosum].

It is suggested that "Corrected value of patients" is a useful method in comparing prefectural surveillance data. "Corrected value of patients" is calculated as follows: Ratio of the number of reported patients for 5 years of each prefecture of each infectious diseases to number of the national scale is called "Corrected rate". The number to be divided is called "Corrected value of patient", individually reported number of patients of the surveillance divided by "Corrected rate". Because the "Corrected value of patients" is based on the number of reported patients for 5 years, the unequality among epidemics which differ become similar. As the value of practical usage is well recognized, 3-dimensional graphs can be used for weekly reports, not only for Exanthema subitum but also for Erythem infectiosum.

[Tissue culture of guinea pig middle ear epithelium--morphological characterization and proliferative activities of cultured cells on fibroblast-reorganized collagen gels].

Long-term culture of the middle ear epithelium of guinea pigs was carried out on reconstituted floating collagen matrix. Fibroblasts established from the abdominal skin dermis of allogenic animals were used to reorganize hydrated collagen gels into a dermal-like matrix. The explants placed on the surface of these matrices were composed of pseudostratified columnar cells with polygonal flat outgrowth sheets, which could be maintained for up to one month. In contrast, with simple hydrated collagen gel, no lysis of the substrate was observed regarding this reorganized collagen gel. In order to examine the growth pattern of these culture cells, 5-bromodeoxyuridine (BrdU) was added to the medium during the entire culture period. The specimens were immunohistologically stained using monoclonal antibodies. Noticeable changes were observed in the marginal portion of the explant where the cell shape changed from cuboidal to squamous. In this transitional area, most cells showed positive staining and consequently high proliferative activity. In the central area of the explants, however, the number of positive cells decreased and the main observation was a few labeled basal cell nuclei. It was suggested that the same regenerative process which usually occurs in normal respiratory epithelia after mechanical injury or other insults, was replayed in this culture system.

Effect of gentamicin intoxication on frog behavior.

Eighty micrograms of Gentamicin were injected into bull frogs' perilymphatic cistern for 3 days. Behavioral changes were evaluated together with morphology of the semicircular canal crista and the utricular macula. The behaviors evaluated were posture, walking, head stability, jumping and swimming. The earliest change of behavior was noticed one day after the last injection, and the changes tended to develop over the following 1 to 2 weeks. When the utricular macula was damaged, the frog tilted toward the damaged side. No tilting was observed when bilateral utricles were intact, or when bilateral utricles were equally damaged. Damage of the posterior (p.v.c.) and anterior vertical canal (a.v.c.) cristae resulted in instability of the head. Jumping ability also deteriorated when the p.v.c. and a.v.c. were damaged. These results indicate that p.v.c. and a.v.c. are involved in head stability and jumping function, while the utricle contributes to perception of gravity.

Identification of dimethyl disulfide-forming bacteria isolated from activated sludge.

Twenty-four strains with high dimethyl disulfide (DMDS)-forming ability were isolated from activated sludge and identified to the genus level. These bacteria were classified into four groups (A, B, C, and D) by the API ZYM System (API System S.A., Montalieu, France). Group A (three strains) was identified as genus Lactobacillus by the API 20B System, by the method of Cowan and Steel, and by production of lactic acid as confirmed by gas-liquid chromatography. Group B (eight strains) was identified as genus Corynebacterium by API 20B and the Cowan and Steel method. Group C (one strain) was suggested to belong to genus Corynebacterium by the API 20B System. Group D (12 strains) was identified as genus Pseudomonas or Alcaligenes by the API 20B System, as genus Alcaligenes by the Cowan and Steel method, and as Achromobacter group Vd by the API 20NE System. However, on the basis of guanine-plus-cytosine contents in DNA and form of flagella, these strains were identified as genus Pseudomonas. Formation of DMDS from DL-methionine and S-methyl-L-cysteine was tested. DMDS-forming bacteria isolated from activated sludge formed DMDS from both precursors. In genus Pseudomonas, P. aeruginosa could not form DMDS from either precursor, but P. acidovorans, P. alcaligenes, P. pseudoalcaligenes, and P. testosteroni formed DMDS. In genus Alcaligenes, A. denitrificans subsp. xylosoxydans, A. denitrificans subsp. denitrificans, A. faecalis, and A. odorans formed DMDS from both precursors. Achromobacter group Vd formed DMDS from S-methyl-L-cysteine, but could not from DL-methionine.