Small variable segments constitute a major type of diversity of bacterial genomes at the species level

Background  

Analysis of large scale diversity in bacterial genomes has mainly focused on elements such as pathogenicity islands, or more generally, genomic islands. These comprise numerous genes and confer important phenotypes, which are present or absent depending on strains. We report that despite this widely accepted notion, most diversity at the species level is composed of much smaller DNA segments, 20 to 500 bp in size, which we call microdiversity.     

Characterization of the AfaD-like family of invasins encoded by pathogenic Escherichia coli associated with intestinal and extra-intestinal infections

The afimbrial adhesive sheath, encoded by the afa-3 gene cluster, is composed of two proteins with different roles in bacterium-HeLa cell interactions. AfaE is required for adhesion and AfaD for internalization. In this study, we found that the AfaD invasin was structurally and functionally conserved among human afa-expressing strains, independently of AfaE subtype and clinical origin of the Escherichia coli isolate. The AggB protein from enteroaggregative E. coli was also found to be an AfaD-related invasin. These data suggest that AfaD is the prototype of a family of invasins encoded by adhesion-associated operons in pathogenic E. coli.     

Nucleotide modifications in three functionally important regions of the Saccharomyces cerevisiae ribosome affect translation accuracy

Important regions of rRNA are rich in nucleotide modifications that can have strong effects on ribosome biogenesis and translation efficiency. Here, we examine the influence of pseudouridylation and 2′-O-methylation on translation accuracy in yeast, by deleting the corresponding guide snoRNAs. The regions analyzed were: the decoding centre (eight modifications), and two intersubunit bridge domains—the A-site finger and Helix 69 (six and five modifications). Results show that a number of modifications influence accuracy with effects ranging from 0.3- to 2.4-fold of wild-type activity. Blocking subsets of modifications, especially from the decoding region, impairs stop codon termination and reading frame maintenance. Unexpectedly, several Helix 69 mutants possess ribosomes with increased fidelity. Consistent with strong positional and synergistic effects is the finding that single deletions can have a more pronounced phenotype than multiple deficiencies in the same region. Altogether, the results demonstrate that rRNA modifications have significant roles in translation accuracy.     

A comparison of the strength of biodiversity effects across multiple functions

In order to predict which ecosystem functions are most at risk from biodiversity loss, meta-analyses have generalised results from biodiversity experiments over different sites and ecosystem types. In contrast, comparing the strength of biodiversity effects across a large number of ecosystem processes measured in a single experiment permits more direct comparisons. Here, we present an analysis of 418 separate measures of 38 ecosystem processes. Overall, 45 % of processes were significantly affected by plant species richness, suggesting that, while diversity affects a large number of processes not all respond to biodiversity. We therefore compared the strength of plant diversity effects between different categories of ecosystem processes, grouping processes according to the year of measurement, their biogeochemical cycle, trophic level and compartment (above- or belowground) and according to whether they were measures of biodiversity or other ecosystem processes, biotic or abiotic and static or dynamic. Overall, and for several individual processes, we found that biodiversity effects became stronger over time. Measures of the carbon cycle were also affected more strongly by plant species richness than were the measures associated with the nitrogen cycle. Further, we found greater plant species richness effects on measures of biodiversity than on other processes. The differential effects of plant diversity on the various types of ecosystem processes indicate that future research and political effort should shift from a general debate about whether biodiversity loss impairs ecosystem functions to focussing on the specific functions of interest and ways to preserve them individually or in combination.     

A Systematic Approach for the Genetic Dissection of Protein Complexes in Living Cells

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Cell structural changes in the needles of Norway spruce exposed to long-term ozone and drought

Effects of ozone and/or drought on Norway spruce needles werestudied using light microscopy and electron microscopy. Saplingswere exposed to ozone in open-top chambers during 1992–1995and also to drought in the late summers of 1993–1995.Samples from current and previous year needles were collectedfive times during 1995. Ozone increased the numbers of peroxisomesand mitochondria, which suggests that defence mechanisms againstoxidative stress were active. The results from peroxisomes suggestthat the oxidative stress was more pronounced in the upper sideof the needles, and those from mitochondria that defence wasmore active in the younger needle generation. Possibly due tothe good nitrogen status and the active defence, no ozone-specificchloroplast alterations were seen. At the end of the season,older needles from ozone treatments had smaller central vacuolescompared with other needles. Cytoplasmic vacuoles around thenucleus were increased by ozone in the beginning of the experiment,and did not increase towards the end of the season as in thecontrols. These results from vacuoles may indicate that ozoneaffected the osmotic properties of the cells. Decreased numberand underdevelopment of sclerenchyma cells and proliferationof tonoplast were related to nutrient imbalance, which was enhancedby drought. Larger vascular cylinders and more effective starchaccumulation before and after the drought periods compensatedfor the reduced water status. Numbers of peroxisomes and mitochondriawere increased in the drought-exposed needles before the onsetof drought treatments of the study year, i.e. these changeswere memory effects. Interactions between ozone and droughtwere few.     

Arsenic,Cadmium and Lead Erythrocyte Concentrations in Men with a High,Moderate and Low Level of Physical Training

Biological Trace Element Research - The aim of the present study was to determine changes occurring in the erythrocyte concentrations of arsenic (As), cadmium (Cd) and lead (Pb) in highly trained...