Genomic divergence of Escherichia coli strains: evidence for horizontal transfer and variation in mutation rates

This report describes the sequencing in the Escherichia coli B genome of 36 randomly chosen regions that are present in most or all of the fully sequenced E. coli genomes. The phylogenetic relationships among E. coli strains were examined, and evidence for the horizontal gene transfer and variation in mutation rates was determined. The overall phylogenetic tree indicated that E. coli B and K-12 are the most closely related strains, with E. coli O157:H7 being more distantly related, Shigella flexneri 2a even more, and E. coli CFT073 the most distant strain. Within the B, K-12, and O157:H7 clusters, several regions supported alternative topologies. While horizontal transfer may explain these phylogenetic incongruities, faster evolution at synonymous sites along the O157:H7 lineage was also identified. Further interpretation of these results is confounded by an association among genes showing more rapid evolution and results supporting horizontal transfer. Using genes supporting the B and K-12 clusters, an estimate of the genomic mutation rate from a long-term experiment with E. coli B, and an estimate of 200 generations per year, it was estimated that B and K-12 diverged several hundred thousand years ago, while O157:H7 split off from their common ancestor about 1.5–2 million years ago [Int Microbiol 2005 8(4):271-278

Understanding the influence of processing conditions on the extraction of rhamnogalacturonan-I “hairy” pectin from sugar beet pulp

Sugar beet pectin is rich in rhamnogalacturonan-I (RG-I) region, which is a potential source of prebiotics. RG-I pectin cannot be extracted the same way as commercial homogalacturan-rich pectin using hot acid. Therefore, this study has explored several alternative methods, including microwave-assisted extraction (MAE) and conventional- solvent extraction (CSE) at atmospheric pressure using different solvents, and microwave-assisted hydrothermal extraction (MAHE) under pressure using water. No conclusive differences in microwave and conventional heating were found with heating rate controlled. The optimum treatment times of both MAE and CSE at 90 °C atmospheric pressure and regardless of the solvents used were 120 min; however, MAHE at 130 °C under pressure can dramatically reduce the time to 10 min. Alcohol-insoluble solids (AIS) extracted using pH13 solvent by MAE had both the highest RG-I yield at 25.3% and purity at 260.2 mg/g AIS, followed by AIS extracts using water by MAHE with 7.5% and 166.7 mg/g AIS respectively

Barriers and facilitators to implementing community outreach work, and inter-professional collaboration with regional partners

Abstract : Objective. Community outreach workers support individuals in accessing the health and community services they require through various forms of proximity approaches. Even though community outreach has been available in the province of Quebec (Canada) for the past 40 years, it is still difficult to implement and sustain, especially with families of young children. The aim of this study was to document barriers and facilitators to implementing community outreach practices, and to describe how such workers collaborate with sectoral (e.g. health care) and inter-sectoral (e.g. municipalities, community organizations, schools) partners. Methodology. We performed a content analysis on 55 scientific and grey literature documents, and transcriptions of 24 individual interviews and 3 focus groups with stakeholders including parents, community outreach workers, health care employees, and inter-sectoral partners. Results. This study reveals four categories of barriers and facilitators to the implementation of community outreach work (i.e. organizational factors, nature of the work and worker-related factors, family-related factors, external factors). With regards to collaboration, community outreach workers deal with various partners. Good inter-professional collaboration is achieved through positive interactions and communication, shared or co-developed activities for the families, co-intervention with families, and strategies to enhance role awareness and inter-sectoral meetings. Conclusion. Results highlighted that many factors interact and can either influence, positively or negatively, the opportunity to implement community outreach work. The collaborative practices identified may help to maximize facilitators and overcome barriers. Advocacy and a better understanding of how to integrate community outreach work within health services while maintaining the workers’ flexibility are needed to sustain this practice

On the genome constitution and evolution of intermediate wheatgrass (Thinopyrum intermedium: Poaceae, Triticeae)

<p>Abstract</p> <p>Background</p> <p>The wheat tribe Triticeae (Poaceae) is a diverse group of grasses representing a textbook example of reticulate evolution. Apart from globally important grain crops, there are also wild grasses which are of great practical value. Allohexaploid intermediate wheatgrass, <it>Thinopyrum intermedium </it>(2n = 6x = 42), possesses many desirable agronomic traits that make it an invaluable source of genetic material useful in wheat improvement. Although the identification of its genomic components has been the object of considerable investigation, the complete genomic constitution and its potential variability are still being unravelled. To identify the genomic constitution of this allohexaploid, four accessions of intermediate wheatgrass from its native area were analysed by sequencing of chloroplast <it>trn</it>L-F and partial nuclear GBSSI, and genomic <it>in situ </it>hybridization.</p> <p>Results</p> <p>The results confirmed the allopolyploid origin of <it>Thinopyrum intermedium </it>and revealed new aspects in its genomic composition. Genomic heterogeneity suggests a more complex origin of the species than would be expected if it originated through allohexaploidy alone. While <it>Pseudoroegneria </it>is the most probable maternal parent of the accessions analysed, nuclear GBSSI sequences suggested the contribution of distinct lineages corresponding to the following present-day genera: <it>Pseudoroegneria</it>, <it>Dasypyrum</it>, <it>Taeniatherum</it>, <it>Aegilops </it>and <it>Thinopyrum</it>. Two subgenomes of the hexaploid have most probably been contributed by <it>Pseudoroegneria </it>and <it>Dasypyrum</it>, but the identity of the third subgenome remains unresolved satisfactorily. Possibly it is of hybridogenous origin, with contributions from <it>Thinopyrum </it>and <it>Aegilops</it>. Surprising diversity of GBSSI copies corresponding to a <it>Dasypyrum</it>-like progenitor indicates either multiple contributions from different sources close to <it>Dasypyrum </it>and maintenance of divergent copies or the presence of divergent paralogs, or a combination of both. <it>Taeniatherum</it>-like GBSSI copies are most probably pseudogenic, and the mode of their acquisition by <it>Th. intermedium </it>remains unclear.</p> <p>Conclusions</p> <p>Hybridization has played a key role in the evolution of the Triticeae. Transfer of genetic material via extensive interspecific hybridization and/or introgression could have enriched the species' gene pools significantly. We have shown that the genomic heterogeneity of intermediate wheatgrass is higher than has been previously assumed, which is of particular concern to wheat breeders, who frequently use it as a source of desirable traits in wheat improvement.</p

Explaining the disjunct distributions of austral plants: The roles of Antarctic and direct dispersal routes

International audienceAim Dispersal explains the disjunct distributions of many austral plant lineages. However, the role of Antarctica is largely uncertain and the routes of dispersal have remained speculative. Based on niche conservatism we can make predictions about the timing of disjunction establishment, as well as the availability of direct transoceanic, Antarctic stepping-stone, and out-of-Antarctica dispersal routes over time. We evaluate these predictions using molecular divergence time estimates for the establishment of disjunct distributions across multiple plant lineages.Location Southern Hemisphere.Methods We estimated the timing of disjunction establishment and determined habitat affinities for 72 austral plant groups. We used Wilcoxon rank sum tests to compare the timing of disjunction establishment between cold and temperate climate lineages for the full data set, as well as within several subsets. We compared our results with those from a literature survey. Results As niche conservatism predicts, the timing of disjunction establishment in cold and temperate climate austral lineages is consistent with the availability of the corresponding habitats over time. Our results also suggest that disjunction establishment has involved a combination of Antarctic and direct dispersal routes. For cold climate lineages, both out-of-Antarctica and direct dispersal routes are required to explain the observed estimates, while stepping stone routes cannot be ruled out. It appears that for these lineages the importance of the three dispersal routes differs with environmental, geographical and temporal context.Main conclusions Both direct and Antarctic dispersal routes are necessary to explain the establishment of contemporary austral distributions. Evidence that some taxa were, until recently, restricted to Antarctica changes how we view the evolutionary histories of austral floras and the lineages they contain. Moreover, that we detect differences in the importance of alternative dispersal routes suggests that long-distance plant dispersal processes can be explicitly incorporated into models of climate change response