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SetterstenRichardPHHSGatekeepersIntermediaries.pdf
No full textBACKGROUND: Many commentators on ‘‘direct-to-consumer’’ genetic risk information have raised concerns that giving results
to individuals with insufficient knowledge and training in genomics may harm consumers, the health care system, and
society. In response, several commercial laboratories offering genomic risk profiling have shifted to more traditional ‘‘direct-to-provider’’ (DTP) marketing strategies, repositioning clinicians as the intended recipients of advertising of laboratory
services and as gatekeepers to personal genomic information. Increasing popularity of next generation sequencing puts a
premium on ensuring that those who are charged with interpreting, translating, communicating and managing commercial
genomic risk information are appropriately equipped for the job. To shed light on their gatekeeping role, we conducted a
study to assess how and why early clinical users of genomic risk assessment incorporate these tools in their clinical practices
and how they interpret genomic information for their patients.
METHODS and FINDINGS: We conducted qualitative in-depth interviews with 18 clinicians providing genomic risk assessment
services to their patients in partnership with DNA Direct and Navigenics. Our findings suggest that clinicians learned most of
what they knew about genomics directly from the commercial laboratories. Clinicians rely on the expertise of the
commercial laboratories without the ability to critically evaluate the knowledge or assess risks.
CONCLUSIONS: DTP service delivery model cannot guarantee that providers will have adequate expertise or sound clinical
judgment. Even if clinicians want greater genomic knowledge, the current market structure is unlikely to build the
independent substantive expertise of clinicians, but rather promote its continued outsourcing. Because commercial
laboratories have the most ‘‘skin in the game’’ financially, genetics professionals and policymakers should scrutinize the
scientific validity and clinical soundness of the process by which these laboratories interpret their findings to assess whether
self-interested commercial sources are the most appropriate entities for gate-keeping genomic interpretation
Schwarz-Bart, Levinas, and Post-Shoah–Postcolonial Gendered Ethics
Get PDFThis article examines the influence of Emmanuel Levinas’s philosophy on the ethical aspects of the life and work of André Schwarz-Bart. The essay is framed through recent re-interest in Schwarz-Bart’s collaborative works with his wife, Simone, as a bridge between Holocaust and postcolonial studies. The publications, arguments, and key points of intersubjective ethics in Levinas’s work that Schwarz-Bart encountered are carefully examined. The argument confronts the critical reception of Levinas’s concepts of the feminine and dwelling to demonstrate how, when seen through a Judaic lens, these notions form a new gendered reading of Schwarz-Bart’s The Last of the Just.This is the publisher’s final pdf. The article is copyrighted by the Purdue Research Foundation and published by Johns Hopkins University Press. It can be found at: http://muse.jhu.edu/journals/modern_fiction_studies/
Ciliate species diversity and host−parasitoid codiversification in Pseudocollinia infecting krill, with description of Pseudocollinia similis sp. nov.
Get PDFAll parasitoid apostome ciliates infecting krill in the northeastern Pacific are currently assigned to the genus Pseudocollinia. Each krill specimen is apparently infected by only 1 Pseudocollinia species. We describe Pseudocollinia similis sp. nov., discovered infecting the krill Thysanoessa spinifera off Oregon, USA. Its protomite-tomite stage resembles that of P. beringensis, which infects T. inermis (type host species), T. longipes, and T. raschii females in the Bering Sea. These ciliates have similar numbers of somatic kineties (18−21 vs. 16−20) and typically have 3 oral kineties. Furthermore, these 2 apostomes are sister species on gene trees based on sequences of small subunit rRNA (0.06% difference) and cytochrome c oxidase subunit 1 (cox1; 30% difference). P. brintoni and P. oregonensis are closely related as a separate group from P. similis and P. beringensis. The similar tree topologies based on the cox1 sequences of 21 host krill individuals representing 6 krill species (Euphausia pacifica, Nyctiphanes simplex, T. inermis, T. longipes, T. raschii, and T. spinifera) and the apostomes isolated from these krill suggest host−parasitoid codiversification. However, this hypothesis was statistically rejected by an approximately unbiased test in which the host tree topology was used to model parasitoid evolution (p ≤ 0.05).Keywords: Oregon, SSUrRNA, Euphausiids, Apostomatida, Cytochrome c oxidase subunit 1, Small subunit rRNA, Cox1This is the publisher’s final pdf. The published article is copyrighted by Inter-Research and can be found at: http://www.int-res.com/journals/dao/dao-home/
Garcia-RuizHernanBotanyPlantPathologyRolesProgramming.pdf
No full textIn eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short
interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target
loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing
response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has
ten AGO genes of which AGO1, AGO2, and AGO7 have been shown to play roles in antiviral
defense. A genetic analysis was used to identify and characterize the roles of AGO proteins
in antiviral defense against Turnip mosaic virus (TuMV) in Arabidopsis. AGO1, AGO2
and AGO10 promoted anti-TuMV defense in a modular way in various organs, with AGO2
providing a prominent antiviral role in leaves. AGO5, AGO7 and AGO10 had minor effects
in leaves. AGO1 and AGO10 had overlapping antiviral functions in inflorescence tissues
after systemic movement of the virus, although the roles of AGO1 and AGO10 accounted
for only a minor amount of the overall antiviral activity. By combining AGO protein immunoprecipitation
with high-throughput sequencing of associated small RNAs, AGO2, AGO10,
and to a lesser extent AGO1 were shown to associate with siRNAs derived from silencing
suppressor (HC-Pro)-deficient TuMV-AS9, but not with siRNAs derived from wild-type
TuMV. Co-immunoprecipitation and small RNA sequencing revealed that viral siRNAs
broadly associated with wild-type HC-Pro during TuMV infection. These results support the
hypothesis that suppression of antiviral silencing during TuMV infection, at least in part, occurs through sequestration of virus-derived siRNAs away from antiviral AGO proteins by
HC-Pro. These findings indicate that distinct AGO proteins function as antiviral modules,
and provide a molecular explanation for the silencing suppressor activity of HC-Pro
Na⁺ intercalation pseudocapacitance in graphene-coupled titanium oxide enabling ultra-fast sodium storage and long-term cycling
Get PDFSodium-ion batteries are emerging as a highly promising technology for large-scale energy storage applications. However, it remains a significant challenge to develop an anode with superior long-term cycling stability and high-rate capability. Here we demonstrate that the Na⁺ intercalation pseudocapacitance in TiO₂/graphene nanocomposites enables high-rate capability and long cycle life in a sodium-ion battery. This hybrid electrode exhibits a specific capacity of above 90mAh g⁻¹ at 12,000mAg⁻¹ (≈36 C). The capacity is highly reversible for more than 4,000 cycles, the longest demonstrated cyclability to date. First-principle calculations demonstrate that the intimate integration of graphene with TiO₂ reduces the diffusion energy barrier, thus enhancing the Na⁺ intercalation pseudocapacitive process. The Na-ion intercalation pseudocapacitance enabled by tailor-deigned nanostructures represents a promising strategy for developing electrode materials with high power density and long cycle life.This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by Nature Publishing Group. The published article can be found at: http://www.nature.com/ncomms/2015/150424/ncomms7929/full/ncomms7929.htm
A genetic linkage map of black raspberry (Rubus occidentalis) and the mapping of Ag (4) conferring resistance to the aphid Amphorophora agathonica
Get PDFBlack raspberry (Rubus occidentalis L.) is a high-value crop in the Pacific Northwest of North America with an international marketplace. Few genetic resources are readily available and little improvement has been achieved through breeding efforts to address production challenges involved in growing this crop. Contributing to its lack of improvement is low genetic diversity in elite cultivars and an untapped reservoir of genetic diversity from wild germplasm. In the Pacific Northwest, where most production is centered, the current standard commercial cultivar is highly susceptible to the aphid Amphorophora agathonica Hottes, which is a vector for the Raspberry mosaic virus complex. Infection with the virus complex leads to a rapid decline in plant health resulting in field replacement after only 3–4 growing seasons. Sources of aphid resistance have been identified in wild germplasm and are used to develop mapping populations to study the inheritance of these valuable traits. We have constructed a genetic linkage map using single-nucleotide polymorphism and transferable (primarily simple sequence repeat) markers for F1 population ORUS 4305 consisting of 115 progeny that segregate for aphid resistance. Our linkage map of seven linkage groups representing the seven haploid chromosomes of black raspberry consists of 274 markers on the maternal map and 292 markers on the paternal map including a morphological locus for aphid resistance. This is the first linkage map of black raspberry and will aid in developing markers for marker-assisted breeding, comparative mapping with other Rubus species, and enhancing the black raspberry genome assembly
TiltonSusanEnvironMoleToxMuscleSegmentHomeobox.pdf
No full textEmbryonic diapause is a reproductive strategy widespread in the animal kingdom. This phenomenon is defined by a temporary arrest in blastocyst growth and metabolic activity within a quiescent uterus without implantation until the environmental and maternal milieu become favorable for pregnancy to progress. We found that uterine Msx expression persists during diapause across species; their inactivation in the mouse uterus results in termination of diapause with the development of implantation-like responses (“pseudoimplantation”) that ultimately succumbed to resorption. To understand the cause of this failure, we compared proteome profiles between floxed and Msx-deleted uteri. In deleted uteri, several functional networks, including transcription/translation, ubiquitin-proteasome, inflammation, and endoplasmic reticulum stress, were dysregulated. Computational modeling predicted intersection of these pathways on an enhanced inflammatory signature. Further studies showed that this signature was reflected in increased phosphorylated IκB levels and nuclear NFκB in deleted uteri. This was associated with enhanced proteasome activity and endoplasmic reticulum stress. Interestingly, treatment with anti-inflammatory glucocorticoid (dexamethasone) reduced the inflammatory signature with improvement of the diapause phenotype. These findings highlight an unexpected role of uterine Msx in limiting aberrant inflammatory responses to maintain embryonic diapause
NooneDCEOASArcticCycloneWaterSupportingInformation.pdf
No full textRapid Arctic warming is associated with important water cycle changes: sea ice loss, increasing atmospheric humidity, permafrost thaw, and water-induced ecosystem changes. Understanding these complex modern processes is critical to interpreting past hydrologic changes preserved in paleoclimate records and predicting future Arctic changes. Cyclones are a prevalent Arctic feature and water vapor isotope ratios during these events provide insights into modern hydrologic processes that help explain past changes to the Arctic water cycle. Here we present continuous measurements of water vapor isotope ratios (δ18O, δ2H, d-excess) in Arctic Alaska from a 2013 cyclone. This cyclone resulted in a sharp d-excess decrease and disproportional δ18O enrichment, indicative of a higher humidity open Arctic Ocean water vapor source. Past transitions to warmer climates inferred from Greenland ice core records also reveal sharp decreases in d-excess, hypothesized to represent reduced sea ice extent and an increase in oceanic moisture source to Greenland Ice Sheet precipitation. Thus, measurements of water vapor isotope ratios during an Arctic cyclone provide a critical processed-based explanation, and the first direct confirmation, of relationships previously assumed to govern water isotope ratios during sea ice retreat and increased input of northern ocean moisture into the Arctic water cycle
Mineral protection of soil carbon counteracted by root exudates
Get PDFMultiple lines of existing evidence suggest that climate change enhances root exudation of organic compounds into soils. Recent experimental studies show that increased exudate inputs may cause a net loss of soil carbon. This stimulation of microbial carbon mineralization ('priming') is commonly rationalized by the assumption that exudates provide a readily bioavailable supply of energy for the decomposition of native soil carbon (co-metabolism). Here we show that an alternate mechanism can cause carbon loss of equal or greater magnitude. We find that a common root exudate, oxalic acid, promotes carbon loss by liberating organic compounds from protective associations with minerals. By enhancing microbial access to previously mineral-protected compounds, this indirect mechanism accelerated carbon loss more than simply increasing the supply of energetically more favourable substrates. Our results provide insights into the coupled biotic-abiotic mechanisms underlying the 'priming' phenomenon and challenge the assumption that mineral-associated carbon is protected from microbial cycling over millennial timescales
Response of Blackberry Cultivars to Fertilizer Source during Establishment in an Organic Fresh Market Production System
Get PDFBlackberry (Rubus ssp. Rubus) cultivars, three trailing types (Marion, Black Diamond, and Obsidian) and one semierect type (Triple Crown), were studied for their response to different types of fertilizer from 2011–12, at a certified organic, grower collaborator site located in Jefferson, OR. Plants were fertilized at a target rate of 50 lb/acre nitrogen (N) each spring using three different sources: 1) a liquid fish and molasses blend (4N–0P–1.7K); 2) pelletized soy (Glycine max) meal (8N–0.4P–1.7K); and 3) pelletized, processed poultry litter (4N–1.3P–2.5K). Plants were drip irrigated, and weeds were managed using a polypropylene, permeable landscape fabric (weed mat). Plant responses were greatly affected by cultivar, whereas the effects of fertilizer type were relatively minor. ‘Triple Crown’ produced the greatest yield in both years, whereas ‘Black Diamond’ and ‘Marion’ had the lowest yield in 2011 and 2012, respectively. ‘Triple Crown’ fruit had the highest percent soluble solids and were the least firm in 2011, whereas ‘Marion’ fruit were the least firm in 2012. Harvest date, within year, affected the fruit quality variables measured in all cultivars. Most soil nutrient levels were within the recommended range for all fertilizer treatments, except for boron (B), which declined to deficient levels in the second year. Fertilizer type had no effect on soil nutrient levels other than fertilization with the fish and molasses blend product increased soil potassium and sodium. Soil nutrient levels were affected by cultivar but varied by year for many nutrients. Primocane leaf tissue nutrient concentrations were above or within recommended standards for most nutrients, except for magnesium (Mg), calcium (Ca), and B, which, depending on the cultivar, were below standards. Over the 2-year study, the blackberry cultivars responded similarly to the three types of organic fertilizer. However, the cost of N varied from 5.35/lb for the pelletized soy meal, and $2.54/lb for the pelletized, processed poultry litter. Supplemental fertilization with B, Mg, and Ca would be required with each fertilizer studied to maintain recommended soil fertility levels