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  • 1
    Language: English
    In: Applied and Environmental Microbiology, Oct, 2008, Vol.74(19-20), p.6427-6436
    Description: A whole-fungus hybridization based on computer-assisted comparative sequence analysis is performed to detect actively growing freshwater fungi with new taxon-specific rRNA-targeting fluorescence in situ hybridization (FISH) probes. The newly developed FISH probes have helped to visualize the growing hyphae and germinating conidia on leaves and in membrane cages.
    Keywords: Fluorescence -- Evaluation ; In Situ Hybridization -- Usage ; Ribosomal Rna -- Research ; Water Molds -- Genetic Aspects ; Water Molds -- Environmental Aspects
    ISSN: 0099-2240
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  • 2
    In: Applied and Environmental Microbiology, 1998, Vol. 64(2), p.496
    Description: A bacterial mixed culture reductively dechlorinating trichlorobenzenes was established in a defined, synthetic mineral medium without any complex additions and with pyruvate as the carbon and energy source. The culture was maintained over 39 consecutive transfers of small inocula into fresh media, enriching the dechlorinating activity. In situ probing with fluorescence-labeled rRNA-targeted oligonucleotide probes revealed that two major subpopulations within the microbial consortium were phylogenetically affiliated with a sublineage within the Desulfovibrionaceae and the gamma subclass of Proteobacteria. The bacterial consortium grew by fermentation of pyruvate, forming acetate, propionate, CO2, formate, and hydrogen. Acetate and propionate supported neither the reduction of trichlorobenzenes nor the reduction of sulfate when sulfate was present. Hydrogen and formate were used for sulfate reduction to sulfide. Sulfate strongly inhibited the reductive dechlorination of trichlorobenzenes. However, when sulfate was depleted in the medium due to sulfate reduction, dechlorination of trichlorobenzenes started. Similar results were obtained when sulfite was present in the cultures. Molybdate at a concentration of 1 mM strongly inhibited the dechlorination of trichlorobenzenes. Cultures supplied with molybdate plus sulfate did not reduce sulfate, but dechlorination of trichlorobenzenes occurred. Supplementation of electron-depleted cultures with various electron sources demonstrated that formate was used as a direct electron donor for reductive dechlorination, whereas hydrogen was not.
    Keywords: Bacteria -- Metabolism ; Chlorobenzenes -- Metabolism;
    ISSN: 0099-2240
    ISSN: 00992240
    E-ISSN: 10985336
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  • 3
    In: Applied and Environmental Microbiology, Nov, 1997, Vol.63(11), p.4164(7)
    Description: The dominant bacterial populations in drinking water biofilms in a municipal drinking water distribution system in Berlin, Germany, are identified. Specific oligonucleotide probes were employed in the in situ investigations. Dominant bacterial species were isolated and characterized phylogenetically. In situ probing of bacteria in their natural environment will provide information regarding phylogenetic identity and in situ distribution correlation.
    Keywords: Drinking Water -- Contamination ; Bacteria -- Identification And Classification
    ISSN: 0099-2240
    E-ISSN: 10985336
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  • 4
    In: Applied and Environmental Microbiology, 2008, Vol. 74(20), p.6427
    Description: New rRNA-targeting oligonucleotide probes permitted the fluorescence in situ hybridization (FISH) identification of freshwater fungi in an Austrian second-order alpine stream. Based on computer-assisted comparative sequence analysis, nine taxon-specific probes were designed and evaluated by whole-fungus hybridizations. Oligonucleotide probe MY1574, specific for a wide range of Eumycota, and the genus (Tetracladium)-specific probe TCLAD1395, as well as the species-specific probes ALacumi1698 (Alatospora acuminata), TRIang322 (Tricladium angulatum), and Alongi340 (Anguillospora longissima), are targeted against 18S rRNA, whereas probes TmarchB10, TmarchC1_1, TmarchC1_2, and AlongiB16 are targeted against the 28S rRNA of Tetracladium marchalianum and Anguillospora longissima, respectively. After 2 weeks and 3 months of exposure of polyethylene slides in the stream, attached germinating conidia and growing hyphae of freshwater fungi were accessible for FISH. Growing hyphae and germinating conidia on leaves and in membrane cages were also visualized by the new FISH probes.
    Keywords: Fresh Water -- Microbiology ; Fungi -- Isolation & Purification ; In Situ Hybridization, Fluorescence -- Methods ; Oligonucleotide Probes -- Genetics;
    ISSN: 0099-2240
    ISSN: 00992240
    E-ISSN: 10985336
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  • 5
    In: Applied and Environmental Microbiology, 2006, Vol. 72(7), p.4829
    Description: A DNA microarray platform for the characterization of bacterial communities in freshwater sediments based on a heterogeneous set of 70 16S rRNA-targeted oligonucleotide probes and directly labeled environmental RNA was developed and evaluated. Application of a simple protocol for the efficient background blocking of aminosilane-coated slides resulted in an improved signal-to-noise ratio and a detection limit of 10 ng for particular 16S rRNA targets. An initial specificity test of the system using RNA from pure cultures of different phylogenetic lineages showed a fraction of false-positive signals of approximately 5% after protocol optimization and a marginal loss of correct positive signals. Subsequent microarray analysis of sediment-related community RNA from four different German river sites suggested low diversity for the groups targeted but indicated distinct differences in community composition. The results were supported by parallel fluorescence in situ hybridization in combination with sensitive catalyzed reporter deposition (CARD-FISH). In comparisons of the data of different sampling sites, specific detection of populations with relative cellular abundances down to 2% as well as a correlation of microarray signal intensities and population size is suggested. Our results demonstrate that DNA microarray technology allows for the fast and efficient precharacterization of complex bacterial communities by the use of standard single-cell hybridization probes and the direct detection of environmental rRNA, also in methodological challenging habitats such as heterogeneous lotic freshwater sediments.
    Keywords: Engineering ; Biology ; Economics;
    ISSN: 0099-2240
    ISSN: 00992240
    E-ISSN: 10985336
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  • 6
    In: Applied and Environmental Microbiology, March, 1994, Vol.60(3), p.792(9)
    Description: A genus-specific 16S rRNA-targeted oligonucleotide probe was designed to study the function of Acinetobacter spp. in situ in the enhanced biological phosphate removal in an anaerobic-aerobic activated sludge system. The expected probe specificity was evident for 66 references strains. The species was showed in both settings in distinct compartments of a sewage treatment plant with improved biological phosphate removal.
    Keywords: Nucleic Acid Probes -- Research ; Ribosomal Rna -- Analysis ; Sewage Sludge -- Analysis
    ISSN: 0099-2240
    E-ISSN: 10985336
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  • 7
    In: Applied and Environmental Microbiology, July, 1993, Vol.59(7), p.2293(6)
    Description: The applicability of using rRNA-targeted oligonucleotide probes for the in situ identification of bacteria in drinking water was investigated. The results showed that both planktonic and surface-associated bacteria could be detected with the probes at a limit of around 10(super 3) to 10(super 4) ribosomes per cell. In addition, the percentage of positive cells were significantly higher at the surfaces than in the planktonic phase, indicating that surface-attached cells are more active than free-living cells.
    Keywords: Bacteria -- Identification And Classification ; Dna Probes -- Usage ; Marine Bacteria ; Aquatic Microbiology
    ISSN: 0099-2240
    E-ISSN: 10985336
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