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Gradient Electrophoresis (gradient + electrophoresis)
Selected AbstractsMonitoring bacterial and archaeal community shifts in a mesophilic anaerobic batch reactor treating a high-strength organic wastewaterFEMS MICROBIOLOGY ECOLOGY, Issue 3 2008Changsoo Lee Abstract Shifts in bacterial and archaeal communities, associated with changes in chemical profiles, were investigated in an anaerobic batch reactor treating dairy-processing wastewater prepared with whey permeate powder. The dynamics of bacterial and archaeal populations were monitored by quantitative real-time PCR and showed good agreement with the process data. A rapid increase in bacterial populations and a high rate of substrate fermentation were observed during the initial period. Growth and regrowth of archaeal populations occurred with biphasic production of methane, corresponding to the diauxic consumption of acetate and propionate. Bacterial community structure was examined by denaturing gel gradient electrophoresis (DGGE) targeting 16S rRNA genes. An Aeromonas -like organism was suggested to be mainly responsible for the rapid fermentation of carbohydrate during the initial period. Several band sequences closely related to the Clostridium species, capable of carbohydrate fermentation, lactate or ethanol fermentation, and/or homoacetogenesis, were also detected. Statistical analyses of the DGGE profiles showed that the bacterial community structure, as well as the process performance, varied with the incubation time. Our results demonstrated that the bacterial community shifted, reflecting the performance changes and, particularly, that a significant community shift corresponded to a considerable process event. This suggested that the diagnosis of an anaerobic digestion process could be possible by monitoring bacterial community shifts. [source] Effects of soil improvement treatments on bacterial community structure and soil processes in an upland grassland soilFEMS MICROBIOLOGY ECOLOGY, Issue 1 2003Neil D. Gray Abstract Temporal temperature gradient electrophoresis (TTGE) analysis of 16S rRNA gene fragments amplified with primers selective for eubacteria and ,-proteobacterial ammonia-oxidising bacteria (AOB) was used to analyse changes in bacterial and AOB community profiles of an upland pasture following soil improvement treatments (addition of sewage sludge and/or lime). Community structure was compared with changes in activity assessed by laboratory measurements of basal respiration and ammonia oxidation potentials, and with measurements of treatment- and time-related changes in soil characteristics. The predominant bacterial populations had a high degree of similarity under all treatment regimens, which was most pronounced early in the growing season. Most of the differences that occurred between soil samples with time could be accounted for by spatial and temporal variation; however, analysis of variance and cluster analysis of similarities between 16S rDNA TTGE profiles indicated that soil improvement treatments exerted some effect on community structure. Lime application had the greatest influence. The impact of soil improvement treatments on autotrophic ammonia oxidation was significant and sustained, especially in soils which had received sewage sludge and lime treatments in combination. However, despite obvious changes in soil characteristics, e.g. pH and soil nitrogen, increasing heterogeneity in the AOB community structure over time obscured the treatment effects observed at the beginning of the experiment. Nevertheless, time series analysis of AOB TTGE profiles indicated that the AOB community in improved soils was more dynamic than in control soils where populations were found to be relatively stable. These observations suggest that the AOB populations exhibited a degree of functional redundancy. [source] Effect of Thymus vulgaris essential oil on intestinal bacterial microbiota of rainbow trout, Oncorhynchus mykiss (Walbaum) and bacterial isolatesAQUACULTURE RESEARCH, Issue 10 2010Paola Navarrete Abstract The application of natural and innocuous compounds has potential in aquaculture as an alternative to antibiotics. We evaluated the effect of diet supplementation with Thymus vulgaris essential oil (TVEO) on the allochthonous microbial composition of rainbow trout. DNA was extracted directly from the intestinal contents, and the V3-V4 regions of the 16S rRNA genes were amplified by PCR. The bacterial composition was analysed using temporal temperature gradient electrophoresis (TTGE). No significant changes (P>0.05) were detected in the TTGE profiles of TVEO-treated trout compared with the controls. The Dice similarity index revealed a high stability (Cs >70%) of the intestinal microbiota in both groups during the 5-week period. Sequence analyses of the TTGE bands revealed the same bacterial composition in both groups, with most bacteria belonging to the Proteobacteria and Firmicutes phyla. The in vitro antibacterial activity of TVEO was assessed using a range of normal intestinal isolates and fish pathogens. The inhibitory concentrations for all the tested bacteria were higher than the TVEO levels used in trout, which may explain the in vivo results. [source] Is there a correlation between bacterial vaginosis and preterm labour in women in the Otago region of New Zealand?AUSTRALIAN AND NEW ZEALAND JOURNAL OF OBSTETRICS AND GYNAECOLOGY, Issue 3 2010Kah Heng LIM Context:, While an association between bacterial vaginosis and preterm labour has been established, the relative contribution of this condition remains controversial. Objective:, To determine whether bacterial vaginosis is likely to be an important contributing factor in preterm births in Otago, New Zealand, a region with a historically high rate of such births. Design and setting:, Women receiving antenatal care from Queen Mary Maternity Services were studied prospectively. Cases were women presenting with preterm labour or premature rupture of membranes. Controls had uncomplicated pregnancies and delivered at term. Patients and methods:, Vaginal swabs from 44 cases and 72 controls were examined by amplification of bacterial 16S rRNA genes followed by denaturing gel gradient electrophoresis. Atopobium vaginae, a bacterial vaginosis-associated bacterium, was detected in a separate polymerase chain reaction. Nugent Gram stain scoring of vaginal swabs from 44 cases and 69 controls was also carried out. Results:, Denaturing gel gradient electrophoresis revealed three major types of band profiles corresponding to normal, intermediate and bacterial vaginosis microflorae. There were significantly more cases with bacterial vaginosis band profiles compared with controls (P = 0.024). More cases had intermediate or bacterial vaginosis Nugent scores compared with controls (P = 0.022). Conversely, controls were more likely to have normal scores than cases (P = 0.022). Atopobium vaginae was equally distributed between the cases and controls. Conclusions:, Women in the Otago region undergoing preterm labour were approximately twice as likely to have a bacterial vaginosis type vaginal microflora as controls. In preterm labour, the incidence of bacterial vaginosis was comparable with that found elsewhere, suggesting that current guidelines for treatment and detection of this condition are appropriate. [source] Coronin is involved in uptake of Mycobacterium bovis BCG in human macrophages but not in phagosome maintenanceCELLULAR MICROBIOLOGY, Issue 12 2001Stephanie Schüller By applying density gradient electrophoresis (DGE) to human macrophages infected with Mycobacterium bovis BCG, we were able to separate three different bacterial fractions representing arrested phagosomes, phagolysosomes and mycobacterial clumps. After further purification of the phagosomal population, we found that isolated phagosomes containing live BCG were arrested in maturation as they exhibited only low amounts of the lysosomal glycoprotein LAMP-1 and processing of the lysosomal hydrolase cathepsin D was blocked. In addition, low amounts of MHC class I and class II molecules and the absence of HLA-DM suggest sequestration of mycobacterial phagosomes from antigen-processing pathways. We further investigated the involvement of the actin-binding protein coronin in intracellular survival of mycobacteria and showed that human coronin, as well as F-actin, were associated with early stages of mycobacterial phagocytosis but not with phagosome maintenance. Therefore, we conclude that the unique DGE migration pattern of arrested phagosomes is not as a result of retention of coronin, but that there are other proteins or lipids responsible for the block in maturation in human macrophages. [source] | ||||||||||