Conservation Genomics of the Declining North American Bumblebee Bombus terricola Reveals Inbreeding and Selection on Immune Genes

The yellow-banded bumblebee Bombus terricola was common in North America but has recently declined and is now on the IUCN Red List of threatened species. The causes of B. terricola’s decline are not well understood. Our objectives were to create a partial genome and then use this to estimate population data of conservation interest, and to determine whether genes showing signs of recent selection suggest a specific cause of decline. First, we generated a draft partial genome (contig set) for B. terricola, sequenced using Pacific Biosciences RS II at an average depth of 35×. Second, we sequenced the individual genomes of 22 bumblebee gynes from Ontario and Quebec using Illumina HiSeq 2500, each at an average depth of 20×, which were used to improve the PacBio genome calls and for population genetic analyses. The latter revealed that several samples had long runs of homozygosity, and individuals had high inbreeding coefficient F, consistent with low effective population size. Our data suggest that B. terricola’s effective population size has decreased orders of magnitude from pre-Holocene levels. We carried out tests of selection to identify genes that may have played a role in ameliorating environmental stressors underlying B. terricola’s decline. Several immune-related genes have signatures of recent positive selection, which is consistent with the pathogen-spillover hypothesis for B. terricola’s decline. The new B. terricola contig set can help solve the mystery of bumblebee decline by enabling functional genomics research to directly assess the health of pollinators and identify the stressors causing declines

Benzodiazepine and z-hypnotic prescribing from acute psychiatric inpatient discharge to long-term care in the community

Background: Benzodiazepine and z-hypnotic prescribing has slowly decreased over the past 20 years, however long-term chronic prescribing still occurs and is at odds with prescribing guidance. Objectives: To identify the pattern of benzodiazepine and z-hypnotic prescribing in psychiatric inpatients at discharge and 12 months post-discharge. Methods: Retrospective observational longitudinal cohort study of patients admitted to two adult psychiatric wards between June and November 2012 (inclusive) who were discharged with a prescription for a benzodiazepine or z-hypnotic drug. Routinely collected prescription data available from NHS Scotland Prescribing Information System was used to identify and follow community prescribing of benzodiazepine and z-hypnotics for a 12 month period post-discharge. Data were entered in Excel® and further analysed using SPSS 23. Ethical approval was not required for this service evaluation however Caldicott Guardian approval was sought and granted. Results: Eighty patients were admitted during the study period however only those patients with a single admission were included for analysis (n=74). Thirty per cent (22/74) of patients were prescribed a benzodiazepine or z-hypnotics at discharge; 14 of whom received ‘long-term’ benzodiazepine and z-hypnotics i.e. continued use over the 12 month period. Seven patients received a combination of anxiolytics and hypnotics (e.g., diazepam plus temazepam or zopiclone). Long-term use was associated with a non-significant increase in median benzodiazepine or z-hypnotic dose, expressed as diazepam equivalents. Conclusions: One in three patients were prescribed a benzodiazepine or z-hypnotics at discharge with 1 in 5 receiving continuous long-term treatment (prescriptions) for 12 months post-discharge. As chronic long-term B-Z prescribing and use still remains an issue, future strategies using routine patient-level prescribing data may support prescribers to review and minimise inappropriate long-term prescribing

Some Secrets of Fluorescent Proteins: Distinct Bleaching in Various Mounting Fluids and Photoactivation of cyan fluorescent proteins at YFP-Excitation

Background
The use of spectrally distinct variants of green fluorescent protein (GFP) such as cyan or yellow mutants (CFP and YFP, respectively) is very common in all different fields of life sciences, e.g. for marking specific proteins or cells or to determine protein interactions. In the latter case, the quantum physical phenomenon of fluorescence resonance energy transfer (FRET) is exploited by specific microscopy techniques to visualize proximity of proteins.

Methodology/Principal Findings
When we applied a commonly used FRET microscopy technique - the increase in donor (CFP)-fluorescence after bleaching of acceptor fluorophores (YFP), we obtained good signals in live cells, but very weak signals for the same samples after fixation and mounting in commercial microscopy mounting fluids. This observation could be traced back to much faster bleaching of CFP in these mounting media. Strikingly, the opposite effect of the mounting fluid was observed for YFP and also for other proteins such as Cerulean, TFP or Venus. The changes in photostability of CFP and YFP were not caused by the fixation but directly dependent on the mounting fluid. Furthermore we made the interesting observation that the CFP-fluorescence intensity increases by about 10 - 15% after illumination at the YFP-excitation wavelength – a phenomenon, which was also observed for Cerulean. This photoactivation of cyan fluorescent proteins at the YFP-excitation can cause false-positive signals in the FRET-microscopy technique that is based on bleaching of a yellow FRET acceptor.

Conclusions/Significance
Our results show that photostability of fluorescent proteins differs significantly for various media and that CFP bleaches significantly faster in commercial mounting fluids, while the opposite is observed for YFP and some other proteins. Moreover, we show that the FRET microscopy technique that is based on bleaching of the YFP is prone to artifacts due to photoactivation of cyan fluorescent proteins under these conditions

Regulating the employment dynamics of domestic supply chains

This paper sheds light on the role that the regulation of primarily domestic, rather than global, supply chains could play in protecting and enhancing standards of workplace health and safety, as well as employment standards more generally. The analysis presented confirms the potential relevance of such regulation in these regards. However, it also reinforces existing evidence pointing to the fact that only very rarely will market-related considerations on their own prompt purchasers to seek to directly influence the employment practices of their suppliers. The paper ends therefore by highlighting a number of key issues relating to the design of regulatory initiatives aimed at protecting and enhancing employment conditions within supply chains

Genetic origins of honey bees (Apis mellifera) on Kangaroo Island and Norfolk Island (Australia) and the Kingdom of Tonga

International audienceAbstractWe examine the origin of honey bee (Apis mellifera) populations in Kangaroo Island (Australia), Norfolk Island (Australia) and the Kingdom of Tonga using a highly polymorphic mitochondrial DNA region and a panel of 37 single nucleotide polymorphisms that assigns ancestry to three evolutionary lineages: Eastern Europe, Western Europe and Africa. We also examine inbreeding coefficients and genetic variation using microsatellites and mitochondrial sequencing. The honey bees of Kangaroo Island have a high proportion of Eastern European ancestry (90.2%), consistent with claims that they are of the subspecies A. m. ligustica. The honey bees of Norfolk Island also had a majority of ancestry from Eastern Europe (73.1%) with some contribution from Western Europe (21.2%). The honey bees of Tonga are mainly of Western European (70.3%) origin with some Eastern European ancestry (27.4%). Despite the suspected severe bottlenecks experienced by these island population, inbreeding coefficients were low

Draft Genome Assembly and Population Genetics of an Agricultural Pollinator, the Solitary Alkali Bee (Halictidae: Nomia melanderi).

Alkali bees (Nomia melanderi) are solitary relatives of the halictine bees, which have become an important model for the evolution of social behavior, but for which few solitary comparisons exist. These ground-nesting bees defend their developing offspring against pathogens and predators, and thus exhibit some of the key traits that preceded insect sociality. Alkali bees are also efficient native pollinators of alfalfa seed, which is a crop of major economic value in the United States. We sequenced, assembled, and annotated a high-quality draft genome of 299.6 Mbp for this species. Repetitive content makes up more than one-third of this genome, and previously uncharacterized transposable elements are the most abundant type of repetitive DNA. We predicted 10,847 protein coding genes, and identify 479 of these undergoing positive directional selection with the use of population genetic analysis based on low-coverage whole genome sequencing of 19 individuals. We found evidence of recent population bottlenecks, but no significant evidence of population structure. We also identify 45 genes enriched for protein translation and folding, transcriptional regulation, and triglyceride metabolism evolving slower in alkali bees compared to other halictid bees. These resources will be useful for future studies of bee comparative genomics and pollinator health research

High sample throughput genotyping for estimating C-lineage introgression in the dark honeybee: an accurate and cost-effective SNP-based tool

The natural distribution of the honeybee (Apis mellifera L.) has been changed by humans in recent decades to such an extent that the formerly widest-spread European subspecies, Apis mellifera mellifera, is threatened by extinction through introgression from highly divergent commercial strains in large tracts of its range. Conservation efforts for A. m. mellifera are underway in multiple European countries requiring reliable and cost-efficient molecular tools to identify purebred colonies. Here, we developed four ancestry-informative SNP assays for high sample throughput genotyping using the iPLEX Mass Array system. Our customized assays were tested on DNA from individual and pooled, haploid and diploid honeybee samples extracted from different tissues using a diverse range of protocols. The assays had a high genotyping success rate and yielded accurate genotypes. Performance assessed against whole-genome data showed that individual assays behaved well, although the most accurate introgression estimates were obtained for the four assays combined (117 SNPs). The best compromise between accuracy and genotyping costs was achieved when combining two assays (62 SNPs). We provide a ready-to-use cost-effective tool for accurate molecular identification and estimation oinfo:eu-repo/semantics/publishedVersio

Imaging in the time of NFD/NSF: do we have to change our routines concerning renal insufficiency?

To date there are potential chronology-based but not conclusive reasons to believe that at least some of the gadolinium complexes play a causative role in the pathophysiology of nephrogenic systemic fibrosis (NSF) or nephrogenic fibrosing dermopathy (NFD). Still, the exact pathogenesis and the risk for patients is unclear beside the obvious connection to moderate to severe renal insufficiency. So far, MR imaging with Gd-enhancement was regarded as the safest imaging modality in these patients—the recent development creates tremendous uncertainty in the MR-community. Nevertheless, one should remember that, despite the over 200 cases of NSF and about 100 with proven involvement of Gd3+, the vast majority of over 200 million patients exposed to gadolinium since the 1980s have tolerated these agents well. Importantly, NSF is a rare disease and does not appear to occur in patients without renal impairment. Many patients and researchers have undergone MR investigations with Gd exposure in the past. For those, it is essential to know about the safety of the agents at normal renal function. We can hope that pharmacoepidemiological and preclinical studies will allow us to better understand the pathophysiology and role of the various MR contrast agents in the near future

Institutional Mergers in Ireland

The importance of knowledge as a driver of social and economic growth and prosperity, and the increasingly competitive “global race for knowledge and talent” (Hazelkorn, Higher Educ Manage Policy 21(1):55–76, 2009) have combined to transform the higher education landscape, forcing national governments and higher education institutions (HEIs) to pursue new ways of addressing the challenges of a multi-polar world order. Rising demand for higher education (HE), as part of the broader shift from elite to mass to universal participation, has led to the emergence of new models of provision. At the same time, many governments face restrictions on public resources due to high levels of public and private debt; accordingly, system-level and institutional restructuring has been contemplated as a way to enhance quality, performance and efficiency

Before and after study of bar workers' perceptions of the impact of smoke-free workplace legislation in the Republic of Ireland

<p>Abstract</p> <p>Background</p> <p><it>Objectives</it>: To compare support for, and perceptions of, the impacts of smoke-free workplace legislation among bar workers in the Republic of Ireland (ROI) pre- and post-implementation, and to identify predictors of support for the legislation.</p> <p>Methods</p> <p><it>Setting</it>: Public houses (pubs) in three areas of the ROI.</p> <p><it>Design</it>: Comparisons pre- and post-implementation of smoke-free workplace legislation.</p> <p><it>Participants</it>: From a largely non-random selection, 288 bar workers volunteered for the baseline survey; 220 were followed up one year later (76.4%).</p> <p><it>Outcome measures: </it>Level of support for the legislation, attitude statements concerning potential impacts of the law and modelled predictors of support for the legislation.</p> <p>Results</p> <p>Pre-implementation 59.5% of participants supported the legislation, increasing to 76.8% post-implementation. Support increased among smokers by 27.3 percentage points from 39.4% to 66.7% (p < 0.001) and among non-smokers by 12.4% percentage points from 68.8% to 81.2% (p = 0.003).</p> <p>Pre-legislation three-quarters of participants agreed that the legislation would make bars more comfortable and was needed to protect workers' health. Post-legislation these proportions increased to over 90% (p < 0.001). However, negative perceptions also increased, particularly for perceptions that the legislation has a negative impact on business (from 50.9% to 62.7%, p = 0.008) and that fewer people would visit pubs (41.8% to 62.7%, p < 0.001). After adjusting for relevant covariates, including responses to the attitude statements, support for the ban increased two to three-fold post-implementation. Regardless of their views on the economic impact, most participants agreed, both pre- and post-implementation, that the legislation was needed to protect bar workers' health.</p> <p>Conclusion</p> <p>Smoke-free legislation had the support of three-quarters of a large sample of bar workers in the ROI. However, this group holds complex sets of both positive and negative perspectives on the legislation. Of particular importance is that negative economic perceptions did not diminish the widely held perception that the ban is needed to protect workers' health.</p