The use of a non-coding region of chloroplast DNA in phylogenetic studies of the subtribeSonchinae (Asteraceae:Lactuceae)

The systematic utility of sequences from a non-coding region of chloroplast DNA (cpDNA) betweenpsbA andtrnH^(GUG) was examined by assessing phylogenetic relationships in subtribeSonchinae (Asteraceae:Lactuceae). Primers constructed against highly conserved regions of tRNA genes were used for PCR amplification and sequencing. ThepsbA-trnH intergenic spacer contains several insertions and deletions (indels) inSonchinae with the length varying from 385 to 450 bp. Sequence divergence ranges from 0.00% to 7.54% withinSonchinae, with an average of 2.4%. Average sequence divergence inSonchus subg.Sonchus is 2.0%, while the mean for subg.Dendrosonchus and its close relatives in Macaronesia (the woodySonchus alliance) is 1.0%. Our results suggest that this region does not evolve rapidly enough to resolve relationships among closely related genera or insular endemics in theAsteraceae. The phylogenetic utility ofpsbA-trnH sequences of the non-coding cpDNA was compared to sequences from the ITS region of nuclear ribosomal DNA. The results suggest that ITS sequences evolve nearly four times faster thanpsbA-trnH intergenic spacer sequences. Furthermore, the ITS sequences provide more variable and phylogenetically informative sites and generate more highly resolved trees with more strongly supported clades, and thus are more suitable for phylogenetic comparisons at lower taxonomic levels than thepsbA-trnH intergenic chloroplast sequences.     

A characterization of internet dating network structures among nordic men who have sex with men

Background

The Internet has become an important venue for seeking sexual partners and may facilitate transmission of sexually transmitted infections.

Methods

We examined a 64-day data log of flirt messages expressing sexual interest among MSM within the Qruiser.com community. We used logistic regression to analyze characteristics of MSM sending and receiving flirt messages and negative binomial regression to examine individual activity and popularity. The structural properties, including the core structure of the flirt network, were analyzed.

Results

The MSM population consisted of approximately 40% homosexuals and 37% bisexuals, while the remaining 23% included men who identified as heterosexual but searched for sex with men and “experimental”. MSM were more likely to send flirt messages if they were homosexual and aged 40+ years; young people aged < 30 years were more likely to receive a flirt. Possession of a webcam was strongly associated with both sending flirt messages and being a flirt target. The distributions of flirts sent (max k_out = 2162) and received (max k_in = 84) were highly heterogeneous. Members in central cores were more likely homosexuals, singles, and aged 31–40 years. The probability of a matched flirt (flirt returned from target) increased from 1% in the outer core to 18% in the central core (core size = 4).

Discussion

The flirt network showed high degree heterogeneity similar to the structural properties of real sexual contact networks with a single central core. Further studies are needed to explore use of webcam for Internet dating.     

Rapid identification of nitrogen-fixing and legume-nodulating Burkholderia species based on PCR 16S rRNA species-specific oligonucleotides

Several novel N₂-fixing Burkholderia species associated with plants, including legume-nodulating species, have recently been discovered. Presently, considerable interest exists in studying the diazotrophic Burkholderia species, both for their ecology and their great potential for agro-biotechnological applications. However, the available methods used in the identification of these Burkholderia species are time-consuming and expensive. In this study, PCR species-specific primers based on the 16S rRNA gene were designed, which allowed rapid, easy, and correct identification of most known N₂-fixing Burkholderia. With this approach, type and reference strains of Burkholderia kururiensis, B. unamae, B. xenovorans, B. tropica, and B. silvatlantica, as well as the legume-nodulating B. phymatum, B. tuberum, B. mimosarum, and B. nodosa, were unambiguously identified. In addition, the PCR species-specific primers allowed the diversity of the diazotrophic Burkholderia associated with field-grown tomato and sorghum plants to be determined. B. tropica and B. xenovorans were the predominant species found in association with tomato, but the occurrence of B. tropica with sorghum plants was practically exclusive. The efficiency of the species-specific primers was validated with the detection of B. tropica and B. xenovorans from DNA directly recovered from tomato rhizosphere soil samples. Additionally, using PCR species-specific primers, all of the legume-nodulating Burkholderia were correctly identified, even from single nodules collected from inoculated common bean plants. These primers could contribute to rapid identification of the diazotrophic and nodulating Burkholderia species associated with important crop plants and legumes, as well as revealing their environmental distribution.     

Pilot Field Trial of the EG95 Vaccine Against Ovine Cystic Echinococcosis in Rio Negro,Argentina: Second Study of Impact

Background

Cystic echinococcosis (CE) is an important zoonotic disease caused by the cestode parasite Echinococcus granulosus. It occurs in many parts of the world where pastoral activities predominate, including the Rio Negro province of Argentina. Although CE control activities have been undertaken in the western regions of Rio Negro for more than two decades, the disease continues to remain prevalent in both the human and livestock animal populations. Vaccination of animal intermediate hosts of CE with the EG95 vaccine may provide a new opportunity to improve the effectiveness of CE control measures, although data are lacking about field application of the vaccine.

Aims

Evaluate the impact of EG95 vaccination in sheep on the transmission of Echinococcus granulosus in a field environment.

Methodology

Two trial sites were established in western Rio Negro province within indigenous communities. Vaccination of lambs born into one trial site was introduced and continued for 6 years. Prior to initiation of the trial, and at the end of the trial, the prevalence of CE in sheep was determined by necropsy. Weaned lambs received two injections of EG95 vaccine, approximately one month apart, and a single booster injection one year later. Vaccination was not implemented at the second trial site. A total of 2725 animals were vaccinated in the first year. Animals from this cohort as well as age-matched sheep from the control area were evaluated by necropsy.

Key results

Introduction of the vaccine led to a statistically significant in the number and size of hydatid cysts in comparison to the situation prior to the introduction of the vaccine, or compared to CE prevalence in the control area where the vaccine was not applied. The prevalence of infection in the vaccinated area was also significantly reduced by 62% compared to the re-intervention level, being lower than the prevalence seen in the control area, although the difference from the control area after the intervention was not significant possibly due to limitations in the numbers of animals available for necropsy.

Conclusions

Vaccination of sheep with the EG95 vaccine provides a valuable new tool which improves the effectiveness of CE control activities. Vaccination was effective even in a difficult, remote environment where only approximately half the lambs born into the communities were fully vaccinated.     

Expression of the S receptor kinase in self-compatible Brassica napus cv. Westar leads to the allele-specific rejection of self-incompatible Brassica napus pollen

Expression of an S receptor kinase (SRK910) transgene in the self-compatible Brassica napus cv. Westar conferred on the transgenic pistil the ability to reject pollen from the self-incompatible Brassica napus W1 line, which carries the S910 allele. In one of the SRK transgenic lines, 1C, virtually no seeds were produced when the transgenic pistils were pollinated with W1 pollen (Mean number of seeds per pod = 1.22). This response was specific to the W1 pollen since pollen from a different self-incompatible Brassica napus line (T2) and self-pollinations were fully compatible. Westar plants expressing an S locus glycoprotein transgene (SLG910) did not show any self-incompatibility response towards W1 pollen. Transgenic Westar plants resulting from crosses between the 1C SRK transgenic line and three SLG910 transgenic lines were also tested for rejection of W1 pollen. The additional expression of the SLG910 transgene in the SRK910 transgenic plants did not cause any significant further reduction in seed production (Mean seeds/pod = 1.04) or have any detectable effects on the number of pollen grains that adhered to the pistil. Thus, while the allele-specific SLG gene was previously reported to have an enhancing effect on the self-incompatibility response, no evidence for such a role was found in this study.     

The origin of bird pollination in Macaronesian Lotus (Loteae, Leguminosae)

The four red-flowered, apparently bird-pollinated Lotus species from the Canary Islands have previously been classified in their own genus, Rhyncholotus. Currently, they are considered as a separate section within genus Lotus, distinct from other herbaceous Canarian congeners which are yellow-flowered and bee-pollinated. A combined analysis of four nuclear regions (including ITS and three homologues of CYCLOIDEA) and three plastid regions (CYB6, matK and trnH-psbA) nests the four bird-pollinated species within a single extant species of bee-pollinated Lotus (L. sessilifolius), in a very extreme example of species paraphyly. Therefore, our data compellingly support the hypothesis that the Macaronesian Lotus species with a bird pollination syndrome are recently derived from entomophilous ancestors. Calibration of the phylogenetic trees using geological age estimates of the most recent islands (La Palma and El Hierro) together with oldest ages of Fuerteventura indicates that bird pollination evolved ca. 1.7 Ma in the Canarian Lotus. These four bird-pollinated species share a most recent common ancestor (MRCA) with L. sessilifolius that dates to about 2.2 Ma. Our analyses further suggest that the evolution of the bird pollination syndrome was likely triggered by the availability of new niches in La Palma and Tenerife as a result of recent volcanic activity.     

About a rare case of intolerance toVicia faba in a non G-6-PD deficient subject

Summary The history of a non G-6-PD deficient woman, who developed a hard intolerance reaction to theVicia fiba ingestion is described.     

Combining gene signatures improves prediction of breast cancer survival

Background

Several gene sets for prediction of breast cancer survival have been derived from whole-genome mRNA expression profiles. Here, we develop a statistical framework to explore whether combination of the information from such sets may improve prediction of recurrence and breast cancer specific death in early-stage breast cancers. Microarray data from two clinically similar cohorts of breast cancer patients are used as training (n = 123) and test set (n = 81), respectively. Gene sets from eleven previously published gene signatures are included in the study.

Principal Findings

To investigate the relationship between breast cancer survival and gene expression on a particular gene set, a Cox proportional hazards model is applied using partial likelihood regression with an L2 penalty to avoid overfitting and using cross-validation to determine the penalty weight. The fitted models are applied to an independent test set to obtain a predicted risk for each individual and each gene set. Hierarchical clustering of the test individuals on the basis of the vector of predicted risks results in two clusters with distinct clinical characteristics in terms of the distribution of molecular subtypes, ER, PR status, TP53 mutation status and histological grade category, and associated with significantly different survival probabilities (recurrence: p = 0.005; breast cancer death: p = 0.014). Finally, principal components analysis of the gene signatures is used to derive combined predictors used to fit a new Cox model. This model classifies test individuals into two risk groups with distinct survival characteristics (recurrence: p = 0.003; breast cancer death: p = 0.001). The latter classifier outperforms all the individual gene signatures, as well as Cox models based on traditional clinical parameters and the Adjuvant! Online for survival prediction.

Conclusion

Combining the predictive strength of multiple gene signatures improves prediction of breast cancer survival. The presented methodology is broadly applicable to breast cancer risk assessment using any new identified gene set.     

Key Processes for Cheirolophus (Asteraceae) Diversification on Oceanic Islands Inferred from AFLP Data

The radiation of the genus Cheirolophus (Asteraceae) in Macaronesia constitutes a spectacular case of rapid diversification on oceanic islands. Twenty species – nine of them included in the IUCN Red List of Threatened Species – have been described to date inhabiting the Madeiran and Canarian archipelagos. A previous phylogenetic study revealed that the diversification of Cheirolophus in Macaronesia started less than 2 Ma. As a result of such an explosive speciation process, limited phylogenetic resolution was reported, mainly due to the low variability of the employed molecular markers. In the present study, we used highly polymorphic AFLP markers to i) evaluate species'' boundaries, ii) infer their evolutionary relationships and iii) investigate the patterns of genetic diversity in relation to the potential processes likely involved in the radiation of Cheirolophus. One hundred and seventy-two individuals representing all Macaronesian Cheirolophus species were analysed using 249 AFLP loci. Our results suggest that geographic isolation played an important role in this radiation process. This was likely driven by the combination of poor gene flow capacity and a good ability for sporadic long-distance colonisations. In addition, we also found some traces of introgression and incipient ecological adaptation, which could have further enhanced the extraordinary diversification of Cheirolophus in Macaronesia. Last, we hypothesize that current threat categories assigned to Macaronesian Cheirolophus species do not reflect their respective evolutionary relevance, so future evaluations of their conservation status should take into account the results presented here.     

Bioactivity of humic acids isolated from vermicomposts at different maturation stages

Background and aims

Vermicomposts are useful to improve environmental quality and sustainable agriculture. Moreover, it is enriched with highly bioactive humic acids (HAs)-like substances and can substitute no-renew source of humic substances to use as plant growth promoters in agriculture. The aim of this work was to evaluate the biological effects of HAs isolated at increasing vermicompost maturation stages.

Methods

Lateral root emergence, aqueous growth medium acidification and proton pumps of maize seedlings were used to monitor HAs bioactivity. Molecular conformation of the HAs was determined by size-exclusion and reverse-phase high performance liquid chromatography. We applied spectroscopy ¹³C-NMR on VC samples to follow the humification process.

Results

We observed a decrease of carbohydrate content and selective preservation of hydrophobic alkyl and aryl C components by ¹³C-NMR during vermicompost maturation. Apparent molecular weight distribution of HAs did not change with vermicompost maturation, but was possible observed increase on hydrophobic moieties.

Conclusion

After 60 days of vermicomposting, all HAs promotes lateral root emergence, acidification of growth aqueous medium and induction of proton pumps without changes on apparent molecular weight but with enhance on hydrophobic domains.