Sequence and functional analyses of Haemophilus spp. genomic islands

Background

A major part of horizontal gene transfer that contributes to the diversification and adaptation of bacteria is facilitated by genomic islands. The evolution of these islands is poorly understood. Some progress was made with the identification of a set of phylogenetically related genomic islands among the Proteobacteria, recognized from the investigation of the evolutionary origins of a Haemophilus influenzae antibiotic resistance island, namely ICEHin1056. More clarity comes from this comparative analysis of seven complete sequences of the ICEHin1056 genomic island subfamily.

Results

These genomic islands have core and accessory genes in approximately equal proportion, with none demonstrating recent acquisition from other islands. The number of variable sites within core genes is similar to that found in the host bacteria. Furthermore, the GC content of the core genes is similar to that of the host bacteria (38% to 40%). Most of the core gene content is formed by the syntenic type IV secretion system dependent conjugative module and replicative module. GC content and lack of variable sites indicate that the antibiotic resistance genes were acquired relatively recently. An analysis of conjugation efficiency and antibiotic susceptibility demonstrates that phenotypic expression of genomic island-borne genes differs between different hosts.

Conclusion

Genomic islands of the ICEHin1056 subfamily have a longstanding relationship with H. influenzae and H. parainfluenzae and are co-evolving as semi-autonomous genomes within the 'supragenomes' of their host species. They have promoted bacterial diversity and adaptation through becoming efficient vectors of antibiotic resistance by the recent acquisition of antibiotic resistance transposons.     

Superiority of gas chromatography/tandem mass spectrometry assay (GC/MS/MS) for estradiol for monitoring of aromatase inhibitor therapy

Currently available radioimmunoassay methods for estradiol in serum lack sufficient sensitivity and precision to monitor estradiol levels in patients placed on third generation aromatase inhibitors. We recently validated a gas chromatography/tandem mass spectrometry assay (GC/MS/MS) for estradiol and determined estrogen levels in normal post-menopausal women and in women with breast cancer before and during administration of aromatase inhibitors. Validation of the GC/MS/MS assay in human plasma and human serum included determination of assay sensitivity (<0.63 pg/ml), precision (all CVs less than 17.8%), recovery (98-103%), and linearity of recovery (R=0.998). Levels of estradiol were lower when assayed by GC/MS/MS compared to RIA under all conditions (7.26+/-4.82 pg/ml versus 11.9+12.0 pg/ml in normal post-menopausal women; 5.88+/-3.43 pg/ml versus 13.8+/-7.5 pg/ml in breast cancer patients prior to treatment; and<0.63 pg/ml versus 5.8+/-4.1 pg/ml during aromatase inhibitor therapy). Fifty-five women treated either with atamestane/toremiphene or letrozole/placebo were monitored for estradiol levels at 4, 8 and 12 weeks of therapy. The mean levels of estradiol during aromatase inhibitor therapy was 5.8+/-4.1 pg/ml as measured by RIA and <0.63 pg/ml by GC/MS/MS. The degree of suppression with the aromatase inhibitors as detected by RIA was 58% versus >89% by GC/MS. These results suggest that most RIA methods detect cross-reacting estrogen metabolites and yield higher measured levels than GC/MS/MS. Several pharmacological and clinical considerations suggest that GC/MS/MS should become the preferred method for monitoring aromatase inhibitor therapy.     

Sulphur stable isotopes can distinguish trophic dependence on sediments and plankton in boreal lakes

1. Stable isotopes of carbon are useful for differentiating between freshwater food chains based on planktonic algae or benthic algae, but are reported to be of limited use for identifying food chains based on sedimentary detritus. Because data from marine systems suggest that stable isotopes of sulphur (δ³⁴S values) have potential in this regard, we tested their utility in freshwater lakes.
2. We found that sulphate in the water column of four boreal lakes was enriched in ³⁴S compared to the sulphur in bulk sediments from these lakes. Furthermore, within a given lake, insects known to feed on sediment (directly or via predation) had δ³⁴S values similar to those of sediment, whereas planktonic and benthic invertebrates known to feed on suspended particles had δ³⁴S values similar to those of sulphate in the water column.
3. Using the stable S isotope values of invertebrates that obtain their S from either the sediment or the water column as end members in a two-source mixing model, we show that two fish species obtain their food from both planktonic and sedimentary sources. Furthermore, model results suggest that, as expected, the more benthic-feeding fish species obtains more of its S from the sediment compartment than does the species that feeds in the water-column.
4. Our results suggest that measurements of stable sulphur isotopes provide a means of distinguishing between members of food chains that are based in the water column from those based on sedimentary detritus. As such, they would be a useful complement to stable C isotopes that are used to distinguish between food chains based on planktonic or benthic algae.     

Complete genome sequence of Brucella suis VBI22, isolated from bovine milk

Brucella suis is the causative agent of swine brucellosis and is known to be able to infect several different hosts, including cattle, dogs, and horses, without causing disease symptoms. Here we report the complete genome sequence of Brucella suis VBI22, which was isolated from raw milk from an infected cow.     

Diet‐dependent female evolution influences male lifespan in a nuptial feeding insect

Theory predicts that lifespan will depend on the dietary intake of an individual, the allocation of resources towards reproduction and the costs imposed by the opposite sex. Although females typically bear the majority of the cost of offspring production, nuptial feeding invertebrates provide an ideal opportunity to examine the extent to which reproductive interactions through gift provisioning impose a cost on males. Here we use experimental evolution in an Australian ground cricket to assess how diet influences male lifespan and how the costs of mating evolve for males. Our findings show that males had significantly shorter lifespans in populations that adapted to a low‐quality diet and that this divergence is driven by evolutionary change in how females interact with males over reproduction. This suggests that the extent of sexual conflict over nuptial feeding may be under‐realized by focusing solely on the consequences of reproductive interactions from the female’s perspective.     

THE EFFECT OF ADDED NITROGEN ON THE RATE OF DECOMPOSITION OF ORGANIC MATTER

(1) N added to decomposing organic matter often has no effect or a negative effect on microbial activity, at least in the long term. More than 60 papers are cited in support of this statement.
(2) The negative effect of N is mainly found with recalcitrant organic matter with a high C/N ratio (straw, wood, etc.), whereas a positive effect of N is common for easily degradable organic material with low C/N ratio.
(3) The negative effect of N could be explained by: (i) N disturbs the outcome of competition between potent and less potent decomposers; (ii) through 'ammonia metabolite repression', N blocks production of certain enzymes, at least in basidiomycetes, and enhances breakdown of the most available cellulose, whereby recalcitrant lignocellulose accumulates; (iii) amino compounds condense with polyphenols and other decomposition products, forming 'browning precursors' which are toxic or inhibitory.
(4) The effect of adding N may depend on the microflora present.
(5) There are indications that some microorganisms have a 'luxury uptake' of N when it is present in sufficient amounts, thereby delaying N mineralization.
(6) The addition of N seems to increase the formation of water-soluble , brown, recalcitrant compounds, but to decrease the amount of humus formed.     

Effects of habitat fragmentation on the timing of Crested Tit Parus cristatus natal dispersal

Crested Tit Parus cristatus young from first broods dispersed 1 week later if they were born in small isolated pine plots ('habitat fragments') compared with individuals in a large pine forest ('continuous habitat'). This delay in dispersal was caused by an extended period between fledging and dispersal. In second broods, the delay was even longer due to the interbrood interval being 9 days longer in habitat fragments. As nestlings in habitat fragments had a lower body-mass, and age at dispersal was negatively correlated with nestling body-mass within each nest, the postponed dispersal from fragments might be explained partly by a lower body-mass. Alternatively, postponed dispersal from fragments could result from a barrier effect caused by reluctance to cross inhospitable habitat.
Immigration by young from first broods into habitat fragments was delayed by approximately 3 weeks, and proportionally more second brood emigrants were recovered in this type of habitat. These results are in agreement with the hypothesis that fragments are second-choice habitat. Early immigrants into continuous habitat had a higher probability of settlement in winter flocks compared with late ones, independent of condition or age. Therefore, Crested Tits born in habitat fragments probably have a lower chance of settling in first-choice habitat.