In situ growth rates and biofilm development of Pseudomonas aeruginosa populations in chronic lung infections

The growth dynamics of bacterial pathogens within infected hosts are a fundamental but poorly understood feature of most infections. We have focused on the in situ distribution and growth characteristics of two prevailing and transmissible Pseudomonas aeruginosa clones that have caused chronic lung infections in cystic fibrosis (CF) patients for more than 20 years. We used fluorescence in situ hybridization (FISH) directly on sputum specimens to examine the spatial distribution of the infecting P. aeruginosa cells. Mucoid variants were present in sputum as cell clusters surrounded by an extracellular matrix, whereas nonmucoid variants were present mainly as dispersed cells. To obtain estimates of the growth rates of P. aeruginosa in CF lungs, we used quantitative FISH to indirectly measure growth rates of bacteria in sputum samples (reflecting the in vivo lung conditions). The concentration of rRNA in bacteria isolated from sputa was measured and correlated with the rRNA contents of the same bacteria growing in vitro at defined rates. The results showed that most cells were actively growing with doubling times of between 100 and 200 min, with some growing even faster. Only a small stationary-phase subpopulation seemed to be present in sputa. This was found for both mucoid and nonmucoid variants despite their different organizations in sputum. The results suggest that the bacterial population may be confronted with selection forces that favor optimized growth activities. This scenario constitutes a new perspective on the adaptation and evolution of P. aeruginosa during chronic infections in CF patients in particular and on long-term infections in general.     

Epidermal growth factor receptor pathway analysis identifies amphiregulin as a key factor for cisplatin resistance of human breast cancer cells

The use of platinum complexes for the therapy of breast cancer is an emerging new treatment modality. To gain insight into the mechanisms underlying cisplatin resistance in breast cancer, we used estrogen receptor-positive MCF-7 cells as a model system. We generated cisplatin-resistant MCF-7 cells and determined the functional status of epidermal growth factor receptor (EGFR), MAPK, and AKT signaling pathways by phosphoreceptor tyrosine kinase and phospho-MAPK arrays. The cisplatin-resistant MCF-7 cells are characterized by increased EGFR phosphorylation, high levels of AKT1 kinase activity, and ERK1 phosphorylation. In contrast, the JNK and p38 MAPK modules of the MAPK signaling pathway were inactive. These conditions were associated with inactivation of the p53 pathway and increased BCL-2 expression. We investigated the expression of genes encoding the ligands for the ERBB signaling cascade and found a selective up-regulation of amphiregulin expression, which occurred at later stages of cisplatin resistance development. Amphiregulin is a specific ligand of the EGFR (ERBB1) and a potent mitogen for epithelial cells. After exposure to cisplatin, the resistant MCF-7 cells secreted amphiregulin protein over extended periods of time, and knockdown of amphiregulin expression by specific short interfering RNA resulted in a nearly complete reversion of the resistant phenotype. To demonstrate the generality and importance of our findings, we examined amphiregulin expression and cisplatin resistance in a variety of human breast cancer cell lines and found a highly significant correlation. In contrast, amphiregulin levels did not significantly correlate with cisplatin resistance in a panel of lung cancer cell lines. We have thus identified a novel function of amphiregulin for cisplatin resistance in human breast cancer cells.     

Method evaluation of Fusarium DNA extraction from mycelia and wheat for down-stream real-time PCR quantification and correlation to mycotoxin levels

Identification of Fusarium species by traditional methods requires specific skill and experience and there is an increased interest for new molecular methods for identification and quantification of Fusarium from food and feed samples. Real-time PCR with probe technology (Taqman) can be used for the identification and quantification of several species of Fusarium from cereal grain samples. There are several critical steps that need to be considered when establishing a real-time PCR-based method for DNA quantification, including extraction of DNA from the samples. In this study, several DNA extraction methods were evaluated, including the DNeasy Plant Mini Spin Columns (Qiagen), the Bio robot EZ1 (Qiagen) with the DNeasy Blood and Tissue Kit (Qiagen), and the Fast-DNA Spin Kit for Soil (Qbiogene). Parameters such as DNA quality and stability, PCR inhibitors, and PCR efficiency were investigated. Our results showed that all methods gave good PCR efficiency (above 90%) and DNA stability whereas the DNeasy Plant Mini Spin Columns in combination with sonication gave the best results with respect to Fusarium DNA yield. The modified DNeasy Plant Mini Spin protocol was used to analyse 31 wheat samples for the presence of F. graminearum and F. culmorum. The DNA level of F. graminearum could be correlated to the level of DON (r(2) = 0.9) and ZEN (r(2) = 0.6) whereas no correlation was found between F. culmorum and DON/ZEA. This shows that F. graminearum and not F. culmorum, was the main producer of DON in Swedish wheat during 2006.     

Acclimation of subsurface microbial communities to mercury

We studied the acclimation to mercury of bacterial communities of different depths from contaminated and noncontaminated floodplain soils. The level of mercury tolerance of the bacterial communities from the contaminated site was higher than those of the reference site. Furthermore, the level of mercury tolerance and functional versatility of bacterial communities in contaminated soils initially were higher for surface soil, compared with the deeper soils. However, following new mercury exposure, no differences between bacterial communities were observed, which indicates a high adaptive potential of the subsurface communities, possibly due to differences in the availability of mercury. IncP-1 trfA genes were detected in extracted community DNA from all soil depths of the contaminated site, and this finding was correlated to the isolation of four different mercury-resistance plasmids, all belonging to the IncP-1beta group. The abundance of merA and IncP-1 plasmid carrying populations increased, after new mercury exposure, which could be the result of selection as well as horizontal gene exchange. The data in this study suggest a role for IncP-1 plasmids in the acclimation to mercury of surface as well as subsurface soil microbial communities.     

Impact of two treatments of a formulation of Beauveria bassiana (Deuteromycota: Hyphomycetes) conidia on Varroa mites (Acari: Varroidae) and on honeybee (Hymenoptera: Apidae) colony health

Bee colonies in southern France were treated with conidia (asexual spores) from two strains of Beauveria bassiana, an entomopathogenic fungus. One strain was commercial (GHA) and the other had been isolated from Varroa mites in the region (Bb05002). Objectives were to evaluate treatment effect on colony weight, adult bee mass, capped brood, and on Varroa fall onto sticky boards. Treatments included conidia formulated with either carnauba or candelilla wax powder, candelilla wax powder alone, or control; in two treatment groups formulation was applied a second time after one week. Treatment did not affect colony health. Colonies treated twice with Bb05002 conidia and carnauba wax powder had significantly higher mite fall compared to colonies treated with blank candelilla wax powder. The proportion of fallen mites that were infected in both conidia treatments was higher than controls for 18 days after the second treatment. The number of fungal propagules on the bees themselves remained elevated for about 14 days after the second treatment. These results were compared to published results from previous experiments with regard to infection duration.     

Cognitive function and symptoms in adults and adolescents in relation to rf radiation from UMTS base stations

There is widespread public concern about the potential adverse health effects of mobile phones in general and their associated base stations in particular. This study was designed to investigate the acute effects of radio frequency (RF) electromagnetic fields (EMF) emitted by the Universal Mobile Telecommunication System (UMTS) mobile phone base stations on human cognitive function and symptoms. Forty adolescents (15-16 years) and 40 adults (25-40 years) were exposed to four conditions: (1) sham, (2) a Continuous Wave (CW) at 2140 MHz, (3) a signal at 2140 MHz modulated as UMTS and (4) UMTS at 2140 MHz including all control features in a randomized, double blinded cross-over design. Each exposure lasted 45 min. During exposure the participants performed different cognitive tasks with the Trail Making B (TMB) test as the main outcome and completed a questionnaire measuring self reported subjective symptoms. No statistically significant differences between the UMTS and sham conditions were found for performance on TMB. For the adults, the estimated difference between UMTS and sham was -3.2% (-9.2%; 2.9%) and for the adolescents 5.5% (-1.1%; 12.2%). No significant changes were found in any of the cognitive tasks. An increase in 'headache rating' was observed when data from the adolescents and adults were combined (P = 0.027), an effect that may be due to differences at baseline. In conclusion, the primary hypothesis that UMTS radiation reduces general performance in the TMB test was not confirmed. However, we suggest that the hypothesis of subjective symptoms and EMF exposure needs further research.     

Genetic determinants of hair and eye colours in the Scottish and Danish populations

Background

The Bovine HapMap Consortium has generated assay panels to genotype ~30,000 single nucleotide polymorphisms (SNPs) from 501 animals sampled from 19 worldwide taurine and indicine breeds, plus two outgroup species (Anoa and Water Buffalo). Within the larger set of SNPs we targeted 101 high density regions spanning up to 7.6 Mb with an average density of approximately one SNP per 4 kb, and characterized the linkage disequilibrium (LD) and haplotype block structure within individual breeds and groups of breeds in relation to their geographic origin and use.

Results

From the 101 targeted high-density regions on bovine chromosomes 6, 14, and 25, between 57 and 95% of the SNPs were informative in the individual breeds. The regions of high LD extend up to ~100 kb and the size of haplotype blocks ranges between 30 bases and 75 kb (10.3 kb average). On the scale from 1–100 kb the extent of LD and haplotype block structure in cattle has high similarity to humans. The estimation of effective population sizes over the previous 10,000 generations conforms to two main events in cattle history: the initiation of cattle domestication (~12,000 years ago), and the intensification of population isolation and current population bottleneck that breeds have experienced worldwide within the last ~700 years. Haplotype block density correlation, block boundary discordances, and haplotype sharing analyses were consistent in revealing unexpected similarities between some beef and dairy breeds, making them non-differentiable. Clustering techniques permitted grouping of breeds into different clades given their similarities and dissimilarities in genetic structure.

Conclusion

This work presents the first high-resolution analysis of haplotype block structure in worldwide cattle samples. Several novel results were obtained. First, cattle and human share a high similarity in LD and haplotype block structure on the scale of 1–100 kb. Second, unexpected similarities in haplotype block structure between dairy and beef breeds make them non-differentiable. Finally, our findings suggest that ~30,000 uniformly distributed SNPs would be necessary to construct a complete genome LD map in Bos taurus breeds, and ~580,000 SNPs would be necessary to characterize the haplotype block structure across the complete cattle genome.     

Gene expression profiles of mouse spermatogenesis during recovery from irradiation

Background  

Irradiation or chemotherapy that suspend normal spermatogenesis is commonly used to treat various cancers. Fortunately, spermatogenesis in many cases can be restored after such treatments but knowledge is limited about the re-initiation process. Earlier studies have described the cellular changes that happen during recovery from irradiation by means of histology. We have earlier generated gene expression profiles during induction of spermatogenesis in mouse postnatal developing testes and found a correlation between profiles and the expressing cell types. The aim of the present work was to utilize the link between expression profile and cell types to follow the cellular changes that occur during post-irradiation recovery of spermatogenesis in order to describe recovery by means of gene expression.     

Pollination crisis in the butterfly-pollinated wild carnation Dianthus carthusianorum?

Knowledge of pollination services provided by flower visitors is a prerequisite for understanding (co)evolutionary processes between plants and their pollinators, for evaluating the degree of specialization in the pollination system, and for assessing threats from a potential pollination crisis. This study examined pollination efficiency and visitation frequency of pollinators--key traits of pollinator-mediated fecundity--in a natural population of the wild carnation Dianthus carthusianorum. The five lepidopteran pollinator species observed differed in pollination efficiency and visitation frequency. Pollinator importance, the product of pollination efficiency and visitation frequency, was determined by the pollinator's visitation frequency. Pollination of D. carthusianorum depended essentially on only two of the five recorded pollinator species. Seed set was pollen-limited and followed a saturating dose-response function with a threshold of c. 50 deposited pollen grains for fruit development. Our results confirm that D. carthusianorum is specialized to lepidopteran pollinators, but is not particularly adapted to the two main pollinator species identified. The local persistence of D. carthusianorum is likely to be at risk as its reproduction depends essentially on only two of the locally abundant, but generally vulnerable, butterfly species.     

TOPping up ATR activity

The nuclear protein kinase ATR is a key regulator of genome integrity that functions at checkpoints for damaged or incompletely replicated DNA. In this issue of Cell, Kumagai et al. (2006) shed light on the molecular mechanism that controls ATR. They report that a physical interaction between ATR and a distinct domain of TopBP1 greatly enhances ATR kinase activity.