Chimeric padlock and iLock probes for increased efficiency of targeted RNA detection

Many approaches exist to detect RNA using complementary oligonucleotides. DNA ligation-based techniques can improve discrimination of subtle sequence variations, but they have been difficult to implement for direct RNA analysis due to the infidelity and inefficiency of most DNA ligases on RNA. In this report, we have systematically studied if ribonucleotide substitutions in padlock probes can provide higher catalytic efficiencies for Chlorella virus DNA ligase (PBCV-1 DNA ligase) and T4 RNA ligase 2 (T4Rnl2) on RNA. We provide broad characterization of end-joining fidelity for both enzymes in RNA-templated 3'-OH RNA/5'-pDNA chimeric probe ligation. Both ligases showed increased ligation efficiency toward chimeric substrates on RNA. However, end-joining fidelity of PBCV-1 DNA ligase remained poor, while T4Rnl2 showed a somewhat better end-joining fidelity compared to PBCV-1 DNA ligase. The recently presented invader padlock (iLock) probes overcome the poor end-joining fidelity of PBCV-1 DNA ligase by the requirement of target-dependent 5' flap removal prior to ligation. Here we show that two particular ribonucleotide substitutions greatly improve the activation and ligation rate of chimeric iLock probes on RNA. We characterized the end-joining efficiency and fidelity of PBCV-1 DNA ligase and T4Rnl2 with chimeric iLock probes on RNA and found that both enzymes exhibit high ligation fidelities for single nucleotide polymorphisms on RNA. Finally, we applied the chimeric probe concept to directly differentiate between human and mouse ACTB mRNA in situ, demonstrating chimeric padlock and iLock probes as superior to their DNA equivalents.

Wherefrom and whereabouts of an alien: the American liver fluke Fascioloides magna in Austria: an overview

The giant liver fluke Fascioloides magna, an invasive species originating from North America, was recorded in Austria in the wild for the first time in 2000. Since then, various data concerning the epidemiology in snail intermediate hosts and cervid final hosts have been reported. Galba truncatula acts as snail intermediate host, and red deer, roe deer and fallow deer act as final hosts. G. truncatula is abundant throughout the region, especially along muddy shores of slow-flowing branches of the river system. Prevalence in deer (20-100 %) is much higher than in snails (0.03-0.2 %). Despite medical treatment of parts of the deer population, the parasite has successfully established itself on both sides of the Danube floodplain environments southeast of Vienna. Genetic analysis revealed that the infection of Austrian deer populations apparently originated from foci in the Czech Republic or from populations of Danube tributaries. Areas adjacent southwards, which will soon be joined through wildlife crossings, have not yet evidenced F. magna. Nonetheless, these environments are inhabited by host snails and deer and therefore constitute suitable habitats for F. magna. Invading alien parasites not only threaten native individual hosts but also influence host populations, thus potentially also modifying parasite communities and interactions. The host range of F. magna includes a variety of potential hosts, notably other Lymnaeidae as potential intermediate hosts and various ungulates, including sheep and cattle, as final hosts. Because eradication after medical treatment was unsuccessful, and due to the risk of further spread of the parasite into unaffected regions, enhanced control strategies need to be developed. We recommend assessment of introduction pathways and dispersal, continuous monitoring of host abundance and distribution and the prevalence of flukes in intermediate and final hosts, as well as coordinated and concerted actions with neighbouring countries. This strategy could help to reduce potential negative impacts of this and other invasive parasites on host populations in Europe.

Sexual reproduction of the pentaploid, short-styled Oxalis pes-caprae allows the production of viable offspring

Reproduction is a key factor for the successful establishment and spread of introduced species. Oxalis pes-caprae is a tristylous species with a self- and morph-incompatibility sexual system that, in the invaded range of the western Mediterranean Basin, has been found to reproduce asexually because only the pentaploid, short-styled morph (5x S-morph) was introduced. The objective of this study was to test the ability of the 5x S-morph of O. pes-caprae to produce viable offspring in the absence of compatible mates, exploring the hypothesis that new morphs could have emerged by sexual reproduction events of the initially introduced morph. Pollen germination, pollen tube development, fruit and seed production, seed germination and offspring ploidy levels were analysed after controlled hand-pollinations to assess self- and morph-incompatibility and production of viable gametes by the 5x S-morph. The self-incompatibility system is still operating, but a partial breakdown in the morph-incompatibility system combined with the production of viable gametes was observed, allowing sexual reproduction of the 5x S-morph in the invaded range. The ability of the 5x S-morph to reproduce sexually may have major consequences for the dynamics of invasive populations of O. pes-caprae and could be one of the factors involved in the occurrence of new floral morphs in this invaded range.