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  • Oxford Journals (Oxford University Press)  (10)
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  • 1
    In: FEMS Microbiology Ecology, 2006, Vol. 56(1), pp.79-94
    Description: The microbial communities of three different habitat types and from two sediment depths in the River Elbe were investigated by fluorescence in situ hybridization at various levels of complexity. Differences in the microbial community composition of free-flowing river water, water within the hyporheic interstitial and sediment-associated bacteria were quantitatively analyzed using domain- and group-specific oligonucleotide probes. Qualitative data on the presence/absence of specific bacterial taxa were gathered using genus- and species-specific probes. The complete data set was statistically processed by univariate statistical approaches, and two-dimensional ordinations of nonmetric multidimensional scaling. The analysis showed: (1) that the resolution of microbial community structures at microenvironments, habitats and locations can be regulated by targeted application of oligonucleotides on phylogenetic levels ranging from domains to species, and (2) that an extensive qualitative presence/absence analysis of multiparallel hybridization assays enables a fine-scale apportionment of spatial differences in microbial community structures that is robust against apparent limitations of fluorescence in situ hybridization such as false positive hybridization signals or inaccessibility of in situ oligonucleotide probes. A general model for the correlation of the phylogenetic depth of focus and the relative spatial resolution of microbial communities by fluorescence in situ hybridization is presented.
    Keywords: Fluorescence Hybridization ; Microbial Communities ; Multivariate Statistics ; Rivers ; Sediments
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 2
    In: FEMS Microbiology Ecology, 2008, Vol. 66(2), pp.282-294
    Description: The secretion of extracellular polymeric substances (EPS) by bacteria has been recognized as important across a wide range of scientific disciplines, but in natural sediments, EPS production by microalgae as a mechanism of sediment stabilization has received much more attention than bacterial products. In the present study, the stabilization potential of a natural benthic bacterial assemblage was tested in cultures growing on noncohesive glass beads. The surface erosion resistance as determined by a cohesive strength meter was significantly enhanced over time compared with controls. Nutrient enrichment of the bacterial assemblages by a general broth (bacteria+) resulted in enhanced stabilization (× 3.6) compared with nutrient-depleted (bacteria) assemblages (× 1.8). This correlated with higher bacterial biomass and EPS concentrations in enriched cultures. Substratum stability was closely related to bacterial cell numbers ( R 2 =0.75/0.78) and EPS protein concentrations ( R 2 =0.96/0.53) (for bacteria/bacteria+ treatments, respectively), but not to EPS carbohydrates. This study implies a greater significance of extracellular proteins in substratum cohesion within the EPS complex than recognized previously. The data show both the importance of bacterial assemblages for microbial sediment stabilization and that a change in abiotic conditions can significantly affect sediment stabilization.
    Keywords: Extracellular Polymeric Substances ; Bacterial Engineering ; Sediment Stability ; Sediment Erosion
    ISSN: 01686496
    E-ISSN: 1574-6941
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  • 3
    In: FEMS Microbiology Reviews, December 2000, Vol.24(5), pp.661-671
    Description: Biofilms, accumulations of microorganisms at interfaces, have been described for every aqueous system supporting life. The structure of these microbial communities ranges from monolayers of scattered single cells to thick, mucous structures of macroscopic dimensions (microbial mats; algal‐microbial associations; trickling filter biofilms). During recent years the structure of biofilms from many different environments has been documented and evaluated by use of a broad variety of microscopic, physico‐chemical and molecular biological techniques, revealing a generally complex 3D structure. Parallel to these investigations more and more complex mathematical models and simulations were developed to explain the development, structures, and interactions of biofilms. The forces determining the spatial structure of biofilms, including microcolonies, extracellular polymeric substances (EPS), and channels, are still the subject of controversy. To achieve conclusive explanations for the structures observed in biofilms the cooperation of both fields of investigation, modelling and experimental research, is necessary. The expanding field of molecular techniques not only allows more and more detailed documentation of the spatial distribution of species, but also of functional activities of single cells in their biofilm environment. These new methods will certainly reveal new insights in the mechanisms involved in the developmental processes involved in the formation and behavior of biofilms.
    Keywords: Biofilm ; Structure ; Species Diversity ; Functional Heterogeneity ; Development
    ISSN: 0168-6445
    E-ISSN: 1574-6976
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  • 4
    Language: English
    In: FEMS Microbiology Ecology, 2000, Vol.32(3), pp.215-223
    Description: Abstract The response of sulfate reducing bacteria (SRB) to oxygen stress under oligotrophic conditions in particle-free systems was studied in (i) sterile Berlin drinking water; (ii) mineral medium; and (iii) in coculture experiments with aerobic bacteria. Using a polyphasic approach including anaerobic cultivation, fluorescent in situ hybridization (FISH) and digital image analysis, the behavior of the strains zt3l and zt10e, isolated from Berlin groundwater and affiliated to the family Desulfovibrionaceae, was compared to the type strains Desulfomicrobium baculatum and Desulfovibrio desulfuricans. Anaerobic deep agar dilution series were performed for the determination of cell culturability. FISH and subsequent digital image analysis of probe-conferred fluorescence intensities were used for the assessment of metabolic activity. For the in situ identification of both isolates in coculture tests, two strain-specific oligonucleotides were developed and evaluated. The total cell counts of stressed SRB in drinking water decreased during the course of the assay dependent on the strain. Both environmental isolates could be cultured for a longer period than cells of D. baculatum and D. desulfuricans, respectively. The FISH intensities showed a strain-specific behavior. When exposed to simultaneous oxygen stress and carbon limitation in mineral medium, total cell counts of all four strains remained constant throughout a period of 72 days. The rate of culturability differed between the investigated strains. The decrease of metabolic activity as assessed by FISH was a strain-specific property. Exposure of SRB to oxygen stress and carbon starvation in coculture experiments with Aquabacterium commune resulted in strain dependent prolonged culturability and a delayed decrease of the metabolic activity compared to pure culture tests for all strains tested. Total cell counts of SRB were constant throughout the whole experiment.
    Keywords: Sulfate Reducing Bacterium ; Drinking Water ; Oxygen Stress ; Fluorescent in Situ Hybridization ; Digital Image Analysis ; Environmental Sciences ; Biology
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 5
    Language: English
    In: FEMS Microbiology Ecology, 1997, Vol.22(4), pp.265-279
    Description: Fluorescence-labeled oligonucleotide probes were applied, combined with in situ reduction of the fluorochrome 5-cyano-2,3-ditolyl tetrazolium chloride (CTC), to describe the development of bacterial density, phylogenetic diversity and bacterial metabolic activity during the formation of drinking water biofilms. Polyethylene and glass surfaces exposed to drinking water in a modified Robbins device were rapidly colonized by a biofilm community of phylogenetically diverse prokaryotes, and cell density of the biofilm community was strictly controlled by grazing eukaryotic organisms. In situ hybridization with group-specific rRNA-targeted oligonucleotide probes revealed the following: (i) the prevalence of bacteria belonging to the beta-subclass of Proteobacteria within the bacterial biofilm populations; (ii) differences in the population composition, assessed by phylogenetic probes, depended on the surface properties of the substrata; (iii) the influence of water retention time on variations in population structure; and (iv) the presence of bacteria belonging to the family Legionellaceae associated with grazing protozoa. The metabolic potential of bacteria was assessed during biofilm formation using fluorescence signals after in situ hybridization and the reduction of the redox dye CTC as an indicator of respiratory activity. Respiratory activity and ribosome content of adherent bacterial cells decreased continuously during the early stages of the biofilm. After 35 days the percentage of CTC-reducing cells stabilized at 30%, and the amount of hybridized cells stabilized at 55%, of the initial cell number. To ascertain the amount of dormant, but potentially active cells, we established a new method, defined as probe active counts (PAC). Biofilms were incubated with a mixture of appropriate carbon sources and an antibiotic preventing bacterial cell division, followed by the determination of metabolic activity by in situ hybridization. By this approach the percentage of hybridized cells could be increased from 50% to 80% of total bacterial cell counts in the oligotrophic drinking water biofilms. ; Includes references ; p. 265-279.
    Keywords: Drinking Water Biofilm ; In Situ Hybridization ; Probe Active Count ; Ctc Reduction ; Environmental Sciences ; Biology
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 6
    Language: English
    In: FEMS Microbiology Ecology, 1998, Vol.25(1), pp.43-61
    Description: Abstract A comprehensive panel of ten 16S rRNA targeted oligonucleotides specific for mesophilic sulfate-reducing bacteria (SRB) within the δ-subclass of Proteobacteria was developed as a diagnostic tool and evaluated for its specificity and in situ applicability. Five probes (DSD131, DSBO224, DSV407, DSR651, DSS658) are specific on genus level and five probes identify distinct phylogenetic subbranches within the families Desulfobacteriaceae (DSMA488, DSB985) and Desulfovibrionaceae (DSV214, DSV698, DSV1292). All oligonucleotides were checked for their specificity by computer aided comparative sequence analysis. For in situ application optimal stringency conditions were adjusted for each fluorescence-labelled probe performing whole cell hybridizations using target and non-target organisms. Activated sludge flocs from different stages within the aeration tank of a large municipal wastewater treatment plant were examined by in situ hybridizations with the indocarbocyanine- (Cy3-) labelled SRB-specific probes. The relative abundance and the spatial organization of single SRB were monitored with epifluorescence and confocal laser scanning microscopy. Individual sulfate-reducing cells could be visualized and the number of cells ranged from 0.5 to 8% of the total cell counts within all stages of the activated sludge process and the final clarifier. Cells yielding strong fluorescence signals after hybridization with the newly developed probes were not restricted to anoxic and anaerobic compartments, but were also clearly detectable in the aeration zones of the treatment plant.
    Keywords: Sulfate-Reducing Bacteria ; Activated Sludge ; In Situ Hybridization ; Environmental Sciences ; Biology
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 7
    Language: English
    In: FEMS Microbiology Ecology, 2000, Vol.33(2), pp.157-170
    Description: Abstract Aerobic and anaerobic cultivation techniques, 16S rDNA-based phylogeny, and fluorescent in situ hybridization were used to describe the phylogenetic diversity and physiological versatility of lotic microbial aggregates (‘river snow’) obtained from the river Elbe. In the course of the year the ‘river snow’ community changed. It was characterized by a great bacterial diversity in spring, the predominant occurrence of algae in summer and reduction of the total bacterial cell count in autumn and winter. In all ‘river snow’ samples, more than 70% of the bacteria counted with the general DNA stain DAPI also hybridized with the Bacteria-specific probe EUB338. In situ analysis of the bacterial ‘river snow’ community with a comprehensive suite of specific rRNA-targeted probes revealed population dynamics to be governed by seasonal factors. During all seasons, β-Proteobacteria constituted the numerically most important bacterial group forming up to 54% of the total cell counts. In contrast to this, the relative abundance of other major bacterial lineages ranged from 2% for the order Planctomycetales to 36% for Cytophaga-Flavobacteria. Cultivation of ‘river snow’ under aerobic and anaerobic conditions with a variety of different media resulted in the isolation of 40 new bacterial strains. Phenotypic and phylogenetic analyses revealed these new strains to be mostly unknown organisms affiliated to different bacterial phyla. Application of newly developed specific oligonucleotide probes proved the cultivated bacteria, including clostridia and the numerically abundant β-Proteobacteria, as relevant in situ members of the ‘river snow’ community.
    Keywords: Lotic System ; River Elbe ; ‘river Snow’ ; Microbial Dynamics ; Fluorescent in Situ Hybridization ; Cultivation ; Molecular Microbial Ecology ; Environmental Sciences ; Biology
    ISSN: 0168-6496
    E-ISSN: 1574-6941
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  • 8
    Language: English
    In: Journal of Crohn's and Colitis, 06/28/2018, Vol.12(7), pp.811-818
    Description: Abstract Objectives Previous population-based studies in patients with ulcerative colitis [UC] revealed variable colectomy rates and colectomy-associated risk factors. Over the past two decades, a decrease in colectomy rates was observed. We assessed risk factors and colectomy rates over time in UC in the Swiss Inflammatory Bowel Disease Cohort Study [SIBDCS]. Methods Prospectively collected SIBDCS data, including disease history, baseline characteristics at enrolment, and course of disease, were retrospectively analysed. Cumulative and adjusted annual colectomy rates were calculated. Results Among 1245 UC patients analysed [54.6% male], 114 [9.2%] underwent colectomy. We observed 5-, 10-, 15-, and 20-year cumulative colectomy rates after diagnosis of 4.1%, 6.4%, 10.4%, and 14.4% of patients, respectively. Male sex (odds ratio [OR] 1.54; p = 0.035), pancolitis at diagnosis [OR = 2.16; p = 0.005], younger age at diagnosis [OR 0.89 per 5 years of age; p = 0.006] and presence of extraintestinal manifestations [EIM] [OR 2.30; p 〈 0.001] were risk factors for undergoing colectomy. We did not observe a significant protective effect of smoking on colectomy risk [OR 0.64; p = 0.106]. The majority of colectomies were performed within first 10 years of disease onset, with a rapidly decreasing colectomy rate after 15 years. In patients diagnosed after 2003, colectomy was performed much earlier during and individual’s disease course. Nevertheless, we found a significantly decreasing trend in yearly colectomy rates over time after 2005. Conclusions Crude and adjusted colectomy rates in Swiss UC patients were lower than those reported previously in the literature, and decreased over time.
    Keywords: Medicine;
    ISSN: 1873-9946
    E-ISSN: 1876-4479
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  • 9
    In: European Heart Journal, 2014, Vol. 35(29), pp.1932-1948
    Description: AimTo investigate the putative modifying effect of dual antiplatelet therapy (DAPT) use on the incidence of stent thrombosis at 3 years in patients randomized to Endeavor zotarolimus-eluting stent (E-ZES) or Cypher sirolimus-eluting stent (C-SES).Methods and resultsOf 8709 patients in PROTECT, 4357 were randomized to E-ZES and 4352 to C-SES. Aspirin was to be given indefinitely, and clopidogrel/ticlopidine for greater than or equal to 3 months or up to 12 months after implantation. Main outcome measures were definite or probable stent thrombosis at 3 years. Multivariable Cox regression analysis was applied, with stent type, DAPT, and their interaction as the main outcome determinants. Dual antiplatelet therapy adherence remained the same in the E-ZES and C-SES groups (79.6% at 1 year, 32.8% at 2 years, and 21.6% at 3 years). We observed a statistically significant (P = 0.0052) heterogeneity in treatment effect of stent type in relation to DAPT. In the absence of DAPT, stent thrombosis was lower with E-ZES vs. C-SES (adjusted hazard ratio 0.38, 95% confidence interval 0.19, 0.75; P = 0.0056). In the presence of DAPT, no difference was found (1.18; 0.79, 1.77; P = 0.43).ConclusionA strong interaction was observed between drug-eluting stent type and DAPT use, most likely prompted by the vascular healing response induced by the implanted DES system. These results suggest that the incidence of stent thrombosis in DES trials should not be evaluated independently of DAPT use, and the optimal duration of DAPT will likely depend upon stent type (Clinicaltrials.gov number NCT00476957).
    Keywords: Drug - Eluting Stent ; Dual Antiplatelet Therapy ; Stent Thrombosis ; Endothelialization ; Healing ; Sirolimus ; Zotarolimus
    ISSN: 0195-668X
    E-ISSN: 1522-9645
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  • 10
    Language: English
    In: Journal of Crohn's and Colitis, 05/27/2019, Vol.13(6), pp.744-754
    Description: Inflammatory bowel disease [IBD] places an economic strain on health systems due to expensive pharmaceutical therapy, risk of hospitalisation and surgery, and long-term monitoring. The evolving treatment guidelines advocate rapid scale-up to biologic agents in order to improve health outcomes and quality of life. This study evaluated changes in health care utilisation and expenditures for IBD in Switzerland over time. We extracted clinical, patient, and resource consumption data from the Swiss IBD Cohort Study between 2006 and 2016. Average unit costs for IBD-related events were derived from Swiss claims data and pharmaceutical price lists. We used multivariate regression, controlling for patient-level characteristics, to estimate trends and determinants of direct and indirect costs and resource utilisation. We included 2365 adults diagnosed with Crohn's disease [CD; N = 1353] and ulcerative colitis [UC; N = 1012]. From 2006-16, mean health care expenditures per patient per year were 9504 euros [70% drugs, 23% inpatient, 7% outpatient] for CD and 5704 euros [68% drugs, 22% inpatient, 10% outpatient] for UC. Health care costs increased by 7% [CD] and 10% [UC] per year, largely due to rising pharmaceutical expenditures driven by increased biologic agent use. Inpatient, outpatient, and indirect costs fluctuated and did not offset increased pharmaceutical costs. Disease characteristics were important predictors of costs. Increased expenditure for IBD was marked by a shift towards greater pharmaceutical management over the past decade. This study highlights the need to identify cost-effective treatment strategies in the face of increased uptake and expenditures associated with innovative treatments.
    Keywords: Crohn’s Disease ; Ibd ; Health Economics ; Ulcerative Colitis;
    ISSN: 1873-9946
    E-ISSN: 1876-4479
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