Inference on microsatellite mutation processes in the invasive mite, Varroa destructor, using reversible jump Markov chain Monte Carlo

Varroa destructor is a parasitic mite of the Eastern honeybee Apis cerana. Fifty years ago, two distinct evolutionary lineages (Korean and Japanese) invaded the Western honeybee Apis mellifera. This haplo-diploid parasite species reproduces mainly through brother sister matings, a system which largely favors the fixation of new mutations. In a worldwide sample of 225 individuals from 21 locations collected on Western honeybees and analyzed at 19 microsatellite loci, a series of de novo mutations was observed. Using historical data concerning the invasion, this original biological system has been exploited to compare three mutation models with allele size constraints for microsatellite markers: stepwise (SMM) and generalized (GSM) mutation models, and a model with mutation rate increasing exponentially with microsatellite length (ESM). Posterior probabilities of the three models have been estimated for each locus individually using reversible jump Markov Chain Monte Carlo. The relative support of each model varies widely among loci, but the GSM is the only model that always receives at least 9% support, whatever the locus. The analysis also provides robust estimates of mutation parameters for each locus and of the divergence time of the two invasive lineages (67,000 generations with a 90% credibility interval of 35,000-174,000). With an average of 10 generations per year, this divergence time fits with the last post-glacial Korea Japan land separation. (c) 2005 Elsevier Inc. All rights reserved.

Superinfection exclusion and the long-term survival of honey bees in Varroa-infested colonies

Over the past 50 years, many millions of European honey bee (Apis mellifera) colonies have died as the ectoparasitic mite, Varroa destructor, has spread around the world. Subsequent studies have indicated that the mite's association with a group of RNA viral pathogens (Deformed Wing Virus, DWV) correlates with colony death. Here, we propose a phenomenon known as superinfection exclusion that provides an explanation of how certain A. mellifera populations have survived, despite Varroa infestation and high DWV loads. Next-generation sequencing has shown that a non-lethal DWV variant 'type B' has become established in these colonies and that the lethal 'type A' DWV variant fails to persist in the bee population. We propose that this novel stable host-pathogen relationship prevents the accumulation of lethal variants, suggesting that this interaction could be exploited for the development of an effective treatment that minimises colony losses in the future.The ISME Journal advance online publication, 27 October 2015; doi:10.1038/ismej.2015.186.

The impact of traffic emissions on atmospheric ozone and OH: results from QUANTIFY

To estimate the impact of emissions by road, aircraft and ship traffic on ozone and OH in the present-day atmosphere six different atmospheric chemistry models have been used. Based on newly developed global emission inventories for road, ship and aircraft emission data sets each model performed sensitivity simulations reducing the emissions of each transport sector by 5%. The model results indicate that on global annual average lower tropospheric ozone responds most sensitive to ship emissions (50.6%±10.9% of the total traffic induced perturbation), followed by road (36.7%±9.3%) and aircraft exhausts (12.7%±2.9%), respectively. In the northern upper troposphere between 200–300 hPa at 30–60° N the maximum impact from road and ship are 93% and 73% of the maximum effect of aircraft, respectively. The latter is 0.185 ppbv for ozone (for the 5% case) or 3.69 ppbv when scaling to 100%. On the global average the impact of road even dominates in the UTLS-region. The sensitivity of ozone formation per NOx molecule emitted is highest for aircraft exhausts. The local maximum effect of the summed traffic emissions on the ozone column predicted by the models is 0.2 DU and occurs over the northern subtropical Atlantic extending to central Europe. Below 800 hPa both ozone and OH respond most sensitively to ship emissions in the marine lower troposphere over the Atlantic. Based on the 5% perturbation the effect on ozone can exceed 0.6% close to the marine surface (global zonal mean) which is 80% of the total traffic induced ozone perturbation. In the southern hemisphere ship emissions contribute relatively strongly to the total ozone perturbation by 60%–80% throughout the year. Methane lifetime changes against OH are affected strongest by ship emissions up to 0.21 (± 0.05)%, followed by road (0.08 (±0.01)%) and air traffic (0.05 (± 0.02)%). Based on the full scale ozone and methane perturbations positive radiative forcings were calculated for road emissions (7.3±6.2 mWm−2) and for aviation (2.9±2.3 mWm−2). Ship induced methane lifetime changes dominate over the ozone forcing and therefore lead to a net negative forcing (−25.5±13.2 mWm−2).

Persistence of anticancer activity in berry extracts after simulated gastrointestinal digestion and colonic fermentation.

Fruit and vegetable consumption is associated at the population level with a protective effect against colorectal cancer. Phenolic compounds, especially abundant in berries, are of interest due to their putative anticancer activity. After consumption, however, phenolic compounds are subject to digestive conditions within the gastrointestinal tract that alter their structures and potentially their function. However, the majority of phenolic compounds are not efficiently absorbed in the small intestine and a substantial portion pass into the colon. We characterized berry extracts (raspberries, strawberries, blackcurrants) produced by in vitro-simulated upper intestinal tract digestion and subsequent fecal fermentation. These extracts and selected individual colonic metabolites were then evaluated for their putative anticancer activities using in vitro models of colorectal cancer, representing the key stages of initiation, promotion and invasion. Over a physiologically-relevant dose range (0-50 µg/ml gallic acid equivalents), the digested and fermented extracts demonstrated significant anti-genotoxic, anti-mutagenic and anti-invasive activity on colonocytes. This work indicates that phenolic compounds from berries undergo considerable structural modifications during their passage through the gastrointestinal tract but their breakdown products and metabolites retain biological activity and can modulate cellular processes associated with colon cancer.

Tracking (poly)phenol components from raspberries in ileal fluid

The (poly)phenols in ileal fluid after ingestion of raspberries were analysed by targeted and non-targeted LC-MSn approaches. Targeted approaches identified major anthocyanin and ellagitannin components at varying recoveries and with considerable inter-individual variation. Non-targeted LC-MSn analysis using an Orbitrap mass spectrometer gave exact mass MS data which was sifted using a software program to select peaks that changed significantly after supplementation. This method confirmed the recovery of the targeted components but also identified novel raspberry-specific metabolites. Some components (including ellagitannin and previously unidentified proanthocyanidin derivatives) may have arisen from raspberry seeds that survived intact in ileal samples. Other components include potential breakdown products of anthocyanins, unidentified components and phenolic metabolites formed in either the gut epithelia or after absorption into the circulatory system and efflux back into the gut lumen. The possible physiological roles of the ileal metabolites in the large bowel are discussed.

Comparison of in vivo and in vitro digestion on polyphenol composition in lingonberries: potential impact on colonic health

The composition of polyphenols in ileal fluid samples obtained from an ileostomy subject after lingonberry intake was compared with lingonberry extracts obtained after simulated in vitro digestion (IVDL) and subsequent faecal fermentation (IVFL). HPLC-PDA-MS/MS analysis confirmed similar patterns of lingonberry (poly)phenolic metabolism after the in vivo and in vitro digestion, with reduced recovery of anthocyanins and a similar pattern of recovery for proanthocyanidins observed for both methods of digestion. On the other hand, the IVFL sample contained none of the original (poly)phenolic components but was enriched in simple aromatic components. Digested and fermented extracts exhibited significant (P < 0.05) anti-genotoxic (Comet assay), anti-mutagenic (Mutation Frequency assay), and anti-invasive (Matrigel Invasion assay) effects in human cell culture models of colorectal cancer at physiologically-relevant doses (0-50 μg/mL gallic acid equivalents). The ileal fluid induced significant anti-genotoxic activity (P < 0.05), but at a higher concentration (200 μg/mL gallic acid equivalents) than the IVDL. Despite extensive structural modification following digestion and fermentation, lingonberry extracts retained their bioactivity in vitro. This reinforces the need for studies to consider the impact of digestion when investigating bioactivity of dietary phytochemicals.

Diversity in a honey bee pathogen: first report of a third master variant of the Deformed Wing Virus quasispecies

Treatment of emerging RNA viruses is hampered by the high mutation and replication rates that enable these viruses to operate as a quasispecies. Declining honey bee populations have been attributed to the ectoparasitic mite Varroa destructor and its affiliation with Deformed Wing Virus (DWV). In the current study we use next-generation sequencing to investigate the DWV quasispecies in an apiary known to suffer from overwintering colony losses. We show that the DWV species complex is made up of three master variants. Our results indicate that a new DWV Type C variant is distinct from the previously described types A and B, but together they form a distinct clade compared with other members of the Iflaviridae. The molecular clock estimation predicts that Type C diverged from the other variants ~319 years ago. The discovery of a new master variant of DWV has important implications for the positive identification of the true pathogen within global honey bee populations.