BackgroundDetection and preventing entry of exotic viruses and viroids at the border is critical for protecting plant industries trade worldwide. Existing post entry quarantine screening protocols rely on time-consuming biological indicators and/or molecular assays that require knowledge of infecting viral pathogens. Plants have developed the ability to recognise and respond to viral infections through Dicer-like enzymes that cleave viral sequences into specific small RNA products. Many studies reported the use of a broad range of small RNAs encompassing the product sizes of several Dicer enzymes involved in distinct biological pathways. Here we optimise the assembly of viral sequences by using specific small RNA subsets.ResultsWe sequenced the small RNA fractions of 21 plants held at quarantine glasshouse facilities in Australia and New Zealand. Benchmarking of several de novo assembler tools yielded SPAdes using a kmer of 19 to produce the best assembly outcomes. We also found that de novo assembly using 21–25 nt small RNAs can result in chimeric assemblies of viral sequences and plant host sequences. Such non-specific assemblies can be resolved by using 21–22 nt or 24 nt small RNAs subsets. Among the 21 selected samples, we identified contigs with sequence similarity to 18 viruses and 3 viroids in 13 samples. Most of the viruses were assembled using only 21–22 nt long virus-derived siRNAs (viRNAs), except for one Citrus endogenous pararetrovirus that was more efficiently assembled using 24 nt long viRNAs. All three viroids found in this study were fully assembled using either 21–22 nt or 24 nt viRNAs. Optimised analysis workflows were customised within the Yabi web-based analytical environment. We present a fully automated viral surveillance and diagnosis web-based bioinformatics toolkit that provides a flexible, user-friendly, robust and scalable interface for the discovery and diagnosis of viral pathogens.ConclusionsWe have implemented an automated viral surveillance and diagnosis (VSD) bioinformatics toolkit that produces improved viruses and viroid sequence assemblies. The VSD toolkit provides several optimised and reusable workflows applicable to distinct viral pathogens. We envisage that this resource will facilitate the surveillance and diagnosis viral pathogens in plants, insects and invertebrates.Electronic supplementary materialThe online version of this article (doi:10.1186/s12859-016-1428-4) contains supplementary material, which is available to authorized users.

Small birds and bats face strong selection pressure to digest food rapidly in order to reduce digesta mass carried during flight. One mechanism is rapid absorption of a high proportion of glucose via the paracellular pathway (transfer between epithelial cells, not mediated by transporter proteins). Intestinal paracellular permeability to glucose was assessed for two nectarivorous passerines, the Australian New Holland honeyeater (Phylidonyris novaehollandiae) and African white-bellied sunbird (Cinnyris talatala) by measuring the bioavailability of radiolabelled, passively absorbed L-glucose. Bioavailability was high in both species and increased with diet sugar concentration (honeyeaters, 37 and 81% and sunbirds, 53 and 71% for 250 and 1000 mmol l L1 sucrose diets, respectively). We conclude that the relative contribution of paracellular to total glucose absorption increases with greater digesta retention time in the intestine, and paracellular absorption may also be modulated by factors such as intestinal lumen osmolality and interaction with mediated glucose uptake. The dynamic state of paracellular absorption should be taken into account in future studies.

Summary 1.Understanding avian diet preferences reveals a great deal about the birds' digestive physiology and relationships with food plants, and can make a valuable contribution towards directing physiological and ecological research. Importantly, diet preferences are likely to reflect physiological constraints and therefore mechanisms of digestion. 2.We assessed the interaction between diet concentration and sugar-type preferences of three Australian nectarivorous bird species. Each individual bird was offered paired energetically-equivalent diets: a sucrose solution and hexose (1 : 1 mixture of glucose : fructose) solution over a range of diet concentrations from 0·075 to 2 mol L -1 Sucrose Equivalents (SE). 3. Similar patterns were found for all three species. Intake on the most dilute diets was insufficient to maintain energy balance, suggesting that these birds faced physiological constraints on such diets. 4. All three species demonstrated a preference for hexose over sucrose when offered dilute diets, and sucrose (or none) preference on more concentrated diets. The three species differed in terms of when this switch from hexose to sucrose preference took place. Rainbow lorikeets (Psittacidae, c. 135 g body mass) demonstrated hexose preference for diets up to and including 0·75 mol L -1 SE; sucrose was preferred on 2 mol L -1 SE diets. Red wattlebirds (Meliphagidae, c. 105 g) showed hexose preference on only the most dilute (0·075 mol L -1 SE) diet, and sucrose preference on 1 and 2 mol L -1 SE diets. New Holland honeyeaters (Meliphagidae, c. 22 g) preferred hexose on 0·075 and 0·1 mol L -1 SE diets, and their selectivity for sucrose was not statistically significant. We suggest that the switch from hexose preference may be directly related to the digestive capacity of different taxa. 5. Accumulating evidence suggests similar patterns of sugar preferences in various nectarivorous bird lineages. A switch from hexose preference on dilute diets to sucrose preference on concentrated diets has now been shown for hummingbirds, flowerpiercers, sunbirds, honeyeaters and lorikeets. Hexose preference on dilute diets suggests that reduced digesta retention time and low sugar concentration influences sucrose hydrolysis efficiency, whilst absorption rate of monosaccharides is less limiting. Sucrose preference on concentrated diets is more puzzling, but may reflect preference for diets with lower osmolality. Varying preferences suggest that the co-evolutionary relationships between birds and nectar sugar composition are likely to be similarly dynamic and situation dependent.

Orphan drug clinical trials often are adversely affected by a lack of high quality treatment efficacy data that can be reliably compared across large patient cohorts derived from multiple governmental and country jurisdictions. It is critical that these patient data be captured with limited corporate involvement. For some time, there have been calls to develop collaborative, non-proprietary, patient-centric registries for post-market surveillance of aspects related to orphan drug efficacy. There is an urgent need for the development and sustainable deployment of these ‘independent’ registries that can capture comprehensive clinical, genetic and therapeutic information on patients with rare diseases. We therefore extended an open-source registry platform, the Rare Disease Registry Framework (RDRF) to establish an Independent Rare Disease Registry (IRDR). We engaged with an established rare disease community for Gaucher disease to determine system requirements, methods of data capture, consent, and reporting. A non-proprietary IRDR model is presented that can serve as autonomous data repository, but more importantly ensures that the relevant data can be made available to appropriate stakeholders in a secure, timely and efficient manner to improve clinical decision-making and the lives of those with a rare disease.