Extensive DNA inversions in the B. fragilis genome control variable gene expression

The obligately anaerobic bacterium Bacteroides fragilis, an opportunistic pathogen and inhabitant of the normal human colonic microbiota, exhibits considerable within-strain phase and antigenic variation of surface components. The complete genome sequence has revealed an unusual breadth (in number and in effect) of DNA inversion events that potentially control expression of many different components, including surface and secreted components, regulatory molecules, and restriction-modification proteins. Invertible promoters of two different types (12 group 1 and 11 group 2) were identified. One group has inversion crossover (fix) sites similar to the hix sites of Salmonella typhimurium. There are also four independent intergenic shufflons that potentially alter the expression and function of varied genes. The composition of the 10 different polysaccharide biosynthesis gene clusters identified (7 with associated invertible promoters) suggests a mechanism of synthesis similar to the O-antigen capsules of Escherichia coli.     

Effect of diets containing a purified soybean trypsin inhibitor on growth performance,digestive proteases and intestinal histology in juvenile sea bream (Sparus aurata L.)

Juvenile sea bream were fed on diets containing 0.0, 2.0 or 4.0 g kg^?1 of a soybean trypsin inhibitor (SBTI) for 30 days. The growth performance, total protease activity and intestinal histology were studied after 0, 15 and 30 days of dietary treatment. No significant differences were found in the weight gain, specific growth rate (SGR) and feed conversion rate in fish fed on inhibitor‐supplemented diets when compared with those fed on an inhibitor‐free diet. Only the SGR at day 15 decreased significantly with protease inhibitor inclusion, although this effect was not observed at day 30. In relation to proteolytic activity at day 15, the total protease activity in the distal intestine decreased in fish fed on inhibitor‐supplemented diets. Zymograms of these extracts showed that the SBTI reduced the intensity of some proteolytic fractions in the distal intestine. A noticeable reduction in the protease activity of the intestinal content in fish fed on the highest level of soybean inhibitor (4.0 g kg^?1) was also observed. However, at day 30, the inhibition effect on these active bands was not detected, and the total protease activity was similar to that in fish fed on an inhibitor‐free diet. Histological examination revealed no perceptible differences in the intestinal structure between any of the diet groups. In addition, all fish were maintained under experimentation for 10 more days and fed on an inhibitor‐free diet to determine whether the possible effects caused by the protease inhibitor could be reverted. The administration of SBTI‐supplemented diets did not affect sea bream growth performance or intestine histology after 30 days, and only a decrease in the total alkaline protease activity was found at day 15.     

Genetic and environmental variability in total and soluble β-glucan in European oat genotypes

A growing interest in oat (Avena ssp.) soluble fibre (β-glucan) is related to its role in the promotion of human health, and to its utilization in the production of functional foods with increased health benefits. Genetic variability and environmental conditions can exert significant effects on the grain β-glucan content. In this study 658 European oat genotypes grown in different environments in 2008 or 2009 within the European Project “Avena genetic resources for quality in human consumption” were analysed for total β-glucan content; the soluble fraction of β-glucan was also determined in a sub-set of 165 samples. Total β-glucan content ranged from 2.85 to 6.77% d.m. and the soluble fraction from 2.05 to 5.29% d.m. The estimated percentage of the soluble fraction ranged from 50.7 to 87.0%. β-glucan content and solubility were significantly influenced by both genotype and growing environment. Hierarchical cluster analysis allowed accessions with similar β-glucan compositions to be grouped. The accessions with the highest contents of both fractions included Avena sativa varieties from several countries and wild species. Finally, the data obtained were used to develop a NIRS calibration equation to predict the contents of total and soluble β-glucan in both naked and husked genotypes.     

Apple (Malus domestica) and tomato (Lycopersicum esculentum) fruits cell-wall hemicelluloses and xyloglucan degradation during Penicillium expansum infection

We characterized the changes in cell-wall hemicellulosic polysaccharides and the hemicellulose-degrading enzymes associated with apple and tomato fruits infected by Penicillium expansum. Our results showed a reduction in the molecular mass of hemicelluloses, with this reduction being particularly notable in the xyloglucan associated with P. expansum infection. The activation of fungal beta-glucanases was also highlighted. Fruit xyloglucan endotransglucosylase/hydrolase (XTH)-specific activity decreased drastically during the infection process in both apple and tomato fruits. We suggest that XTH reduction during the infection might be related with the fungus attack mechanism. We also suggest that the decrease in activity and the consequent lower xyloglucan endotransglucosylation, together with the increase in endoglucanases, would permit fungal access to the cellulose-xyloglucan network, increase the efficiency of cellulose hydrolysis, and thus facilitate the progress of the fungal infection. The results confirm the importance of hemicellulose degradation in the breakdown of plant cell walls, causing cell-wall loosening, increasing the porosity of the wall, and allowing the colonization of plant tissue.     

Factors limiting denitrification in a Mediterranean riparian forest

In situ denitrification (DNT) and denitrification enzyme activity (DEA) were measured in a Mediterranean riparian forest soil during two periods under contrasting soil moisture conditions in order to investigate the factors that affect denitrification through the year. Results showed that in summer, soil moisture limited denitrification throughout the entire soil profile, whereas in winter, anaerobic conditions in the soil were more favourable for denitrifiers. The potential for denitrification was larger at shallow depths (<30 cm), and neither nitrate nor organic carbon limited denitrification significantly. Some denitrification was measured during winter at depths below 30 cm, suggesting that a reduction of groundwater nitrate could occur in some areas of this riparian forest during the wet period. In summer, low denitrification, together with high mineralization rates, brought about an increase of soil N, which could be leached to the stream channel during rainfall events. This study suggests that Mediterranean riparian soils act as sources or sinks of dissolved nitrogen depending on the period of the year.     

Testicular histomorphometry and the proliferative and apoptotic activities of the seminiferous epithelium in Syrian hamster during spontaneous recrudescence after exposure to short photoperiod

Syrian hamsters are photoperiodic rodents in which reproduction, including testicular function, is stimulated by long photoperiod exposure and curtailed by exposure to a short photoperiod. The objectives of this study were to characterize the testis histomorphometrically and to determine the role of the proliferation and apoptosis phenomena in the recovery of the seminiferous epithelium during spontaneous recrudescence after exposure to short photoperiod. The study was performed using conventional light microscopy, proliferating cell nuclear antigen and terminal deoxynucleotidyl transferase (TdT)‐mediated dUTP in situ nick end labelling staining, image analysis software, and transmission electron microscopy in three recrudescence groups: initial recrudescence (IR), advanced recrudescence (AR) and total recrudescence (TR). The results morphometrically pointed to the gradual recovery of the testicular and tubular volumes, as well as of the seminiferous epithelium. Among the IR and AR groups, the increase in testicular and tubular volumes was accompanied by an increase in tubular diameter and length, with an increase in interstitial volume. From AR to TR, there was an increase in the tubular and total volumes, but, in this case, with a gradual increase in tubular diameter. Recovery of the seminiferous epithelium was accompanied by changes in apoptosis and proliferation activities. The first decreased halfway through the process, and the second remained higher than the control levels throughout the recrudescence stage. Alterations in the spermatozoa were ultrastructurally observed, which indicated that spermiogenesis was not yet completely normal. In conclusion, spontaneous testicular recrudescence in Syrian hamster comprises two histomorphometrical phases: the first related to an increase in tubular length and diameter and interstitial volume and the second depending principally on the gradual increase in tubular diameter. The restoration of the seminiferous epithelium is due to apoptosis reaching normal values in the AR group accompanied by higher proliferative activity than that observed in the Control group.     

Variation in Capsicum annuum revealed by RAPD and AFLP markers

Genetic relationships were examined among thirty-four pepper (Capsicum annuum) cultivars of different types. Two types of PCR-based markers were used, RAPD and AFLP, and their relative effectiveness was compared. A dendrogram based on RAPD markers separated the large-fruited sweet cultivars from the small-fruited pungent peppers, and the former group showed less divergence than the latter. The percentage of polymorphic markers was lower for AFLP than for RAPD markers (13 and 22% respectively). However, AFLP primers amplified on average six times more products than RAPD markers. The average numbers of polymorphic products per primer were 1.6 and 6.5 for RAPD and AFLP primers, respectively, i.e., AFLP primers were four times more efficient than RAPD primers in their ability to detect polymorphism in pepper. While four blocky type cultivars were indistinguishable by RAPD, two AFLP primer pairs were sufficient to distinguish the four cultivars from each other. This revised version was published online in July 2006 with corrections to the Cover Date.     

Assessment of the bacterial community diversity associated with the queen conch Strombus gigas (Linnaeus, 1758) from the Caribbean coast of Colombia using denaturing gradient gel electrophoresis and culturing

The biotic diversity of Strombus gigas has not been thoroughly studied despite the status of the queen conch as an important ecological resource. The bacteria associated with the conch influence their host in several ways, including through the metabolism of nutrients, protection against invasive bacteria and the regulation of the physical conditions. In this study, conventional microbiological methods and molecular tools such as denaturing gradient gel electrophoresis (DGGE) were used to assess the composition of the bacterial communities associated with the queen conch (S. gigas) in wild and captive habitats in Colombia. A genetic analysis of the bacterial communities revealed a high level of diversity based on the large number of bands detected using DGGE. In addition, differences in bacterial community structure were found between the conchs in captivity and the wild populations. The dominant phylogenetic affiliations of the bacteria, as determined using 16S rRNA gene sequencing, were grouped into four classes, namely, Betaproteobacteria (16%), Gammaproteobacteria (70%), Firmicutes (7%) and Actinobacteria (2%). These groups are related to host defence processes and the decomposition of organic matter. The 16S rDNA sequence analysis of the cultured bacteria and the resulting DGGE profiles are useful tools for characterizing the diversity of the bacteria associated with the analyzed conchs.