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Ostertag-Hill_HHMI_BHV-1.pptx
No full textAlthough an efficacious bovine herpesvirus type-1 (BHV-1) vaccine has been used for many years, BHV-1 vaccine-related abortion and respiratory disease have been occurring in a rising number of herds. To investigate whether isolates from BHV-1 vaccination with adverse effects are identical to the wild type virus or vaccine virus, regions of the thymidine kinase (TK) gene prone to mutation were examined. Two sets of PCR primers were used to investigate two unique polymorphisms of the TK gene in 35 BHV-1 isolates. The DNA polymorphisms in the TK gene were determined by Sanger sequencing of PCR amplicons and the sequence was analyzed with Geneious software. All BHV-1 isolates and vaccine were found to have TK genes that are different from the wild type virus. Over 50% of the sequenced BHV-1 isolate has TK genes that are different from vaccine strains, with 27% having genetic variation in region 1 of TK and 55% in region 2 of TK. This study suggests that BHV-1 isolates have genetic similarity with vaccine virus but have variation within TK genes, which may have resulted from mutations occurred within the vaccinated animals or from infection with a strain similar to the vaccine virus
Wheat head armyworm true or false : a tale from the Pacific Northwest
Full text linkThe wheat head armyworm (Faronta diffusa) is a troublesome pest in cereal grains in the Pacific Northwest. This publication describes the life cycle, behavior, distribution, and feeding of the wheat head armyworm. Guidance on identification and control of the pest is also provided.Keywords: wheat head armyworm (WHA), Faronta diffusa, WHAPublished December 2009. A more recent revision exists. Facts and recommendations in this publication may no longer be valid. Please look for up-to-date information in the OSU Extension Catalog: http://extension.oregonstate.edu/catalo
A comparison of selected parametric and imputation methods for estimating snag density and snag quality attributes
Full text linkSnags (standing dead trees) are an essential structural component of forests. Because wildlife use of snags depends on size and decay stage, snag density estimation without any information about snag quality attributes is of little value for wildlife management decision makers. Little work has been done to develop models that allow multivariate estimation of snag density by snag quality class. Using climate, topography, Landsat TM data, stand age and forest type collected for 2356 forested Forest Inventory and Analysis plots in western Washington and western Oregon, we evaluated two multivariate techniques for their abilities to estimate density of snags by three decay classes. The density of live trees and snags in three decay classes (D1: recently dead, little decay; D2: decay, without top, some branches and bark missing; D3: extensive decay, missing bark and most branches) with diameter at breast height (DBH) ≥ 12.7 cm was estimated using a nonparametric random forest nearest neighbor imputation technique (RF) and a parametric two-stage model (QPORD), for which the number of trees per hectare was estimated with a Quasipoisson model in the first stage and the probability of belonging to a tree status class (live, D1, D2, D3) was estimated with an ordinal regression model in the second stage. The presence of large snags with DBH ≥ 50 cm was predicted using a logistic regression and RF imputation. Because of the more homogenous conditions on private forest lands, snag density by decay class was predicted with higher accuracies on private forest lands than on public lands, while presence of large snags was more accurately predicted on public lands, owing to the higher prevalence of large snags on public lands. RF outperformed the QPORD model in terms of percent accurate predictions, while QPORD provided smaller root mean square errors in predicting snag density by decay class. The logistic regression model achieved more accurate presence/absence classification of large snags than the RF imputation approach. Adjusting the decision threshold to account for unequal size for presence and absence classes is more straightforward for the logistic regression than for the RF imputation approach. Overall, model accuracies were poor in this study, which can be attributed to the poor predictive quality of the explanatory variables and the large range of forest types and geographic conditions observed in the data.Keywords: Snag size class, Ordinal regression, Snag density, Snag decay class, Nearest neighbor imputatio
River influences on shelf ecosystems: Introduction and synthesis
Full text linkRiver Influences on Shelf Ecosystems (RISE) is the first comprehensive
interdisciplinary study of the rates and dynamics governing the mixing of river and coastal
waters in an eastern boundary current system, as well as the effects of the resultant plume
on phytoplankton standing stocks, growth and grazing rates, and community structure.
The RISE Special Volume presents results deduced from four field studies and two
different numerical model applications, including an ecosystem model, on the buoyant
plume originating from the Columbia River. This introductory paper provides background
information on variability during RISE field efforts as well as a synthesis of results, with
particular attention to the questions and hypotheses that motivated this research. RISE
studies have shown that the maximum mixing of Columbia River and ocean water occurs
primarily near plume liftoff inside the estuary and in the near field of the plume. Most
plume nitrate originates from upwelled shelf water, and plume phytoplankton species are
typically the same as those found in the adjacent coastal ocean. River-supplied nitrate
can help maintain the ecosystem during periods of delayed upwelling. The plume inhibits
iron limitation, but nitrate limitation is observed in aging plumes. The plume also has
significant effects on rates of primary productivity and growth (higher in new plume
water) and microzooplankton grazing (lower in the plume near field and north of the
river mouth); macrozooplankton concentration (enhanced at plume fronts); offshelf
chlorophyll export; as well as the development of a chlorophyll “shadow zone” off
northern Oregon.Keywords: Columbia River plume, freshwater plume, RIS
The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses
Full text linkThe Plant Ontology (PO;http://www.plantontology.org/" is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to > 110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.Keywords: Plant anatomy, Terpene synthase, Bioinformatics, Comparative genomics, Genome annotation, Ontolog
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No full textThis thesis is an effort to formalize and document some of the changes occuring in the Warwar Valley of Gongola State, Nigeria, West Africa. The documentation will comprise a photographic study over time accompanied by an ethnographic narrative. Information gathered from photographic images, field notes and the anthropological record will then be applied to a cultural-ecological model based on the theory of Julian Steward. The Mambilla people inhabiting the Warwar Valley are changing their traditional agricultural land use patterns and value system due to the influx of new ideas, notably the introduction of a cash economy. This cultural change has affected environmental change, observable in soil erosion
NelsonPeterBotanyPlantPathLichenTraitsSpeciesSupplementaryTableS1.pdf
No full textLichens in the Arctic play important ecological roles. They also face the threats of increasing fire and shrub and tree expansion, exacerbated or caused by climate change. These forces may lead to changes not only in lichen community composition but also in the abundance, diversity and distribution of lichen functional traits. We sought to connect landscape-scale patterns of lichen community composition and traits to environmental gradients to both monitor lichen communities and clarify community-trait-environment relationships. We measured lichens throughout one of the largest and most remote U.S. National Parks within the Arctic. We then analyzed lichen community composition and species richness within ecologically informative lichen trait groups along environmental and vascular vegetation gradients. Macrolichen species richness in 0.4 ha plots averaged 41 species with a total landscape level observed gamma diversity of 262 macrolichen species. Jackknife estimators placed the landscape level macrolichen diversity at 307 to 331 species. A gradient from low-elevation forests to high elevation rocky areas was the dominant ecological gradient as expressed by the lichen community, representing 68% of the variation in species composition. Low-elevation forests hosted more epiphytic lichens characteristic of boreal forests, whereas high-elevation lichen communities were characterized by saxicolous lichens, varying between siliceous, basic or mafic rock types. Along this gradient, species reproducing vegetatively and lichens with filamentous growth form were more frequent in forests while the diversity of traits was highest in alpine habitats. Simple cladoniiform, as opposed to erectly branched fruticose lichens in the genus Cladonia, were the only functional group associated with tussock tundra. Vegetation types differed significantly in lichen species composition and richness and trait richness; characteristic suites of lichen species and traits are associated with the particular vegetation types in the Arctic. We also extended the range of Fuscopannaria abscondita reported new to North America and Zahlbrucknerella calcarea new to Alaska.Keywords: Alaska, growth-form, photobiont, Gates of the Arctic National Park and Preserve, vegetative dispersa
Amenity landownership, land use change and the re-creation of “working landscapes”
Full text linkIn recent years the “working landscape” concept has risen to prominence in popular, academic, and policy discourse surrounding conservation of both natural and cultural values in inhabited landscapes. Despite its implied reconciliation of commodity production and environmental protection, this concept remains contested terrain, masking tensions over land use practices and understandings of human-nature relations. Here we draw on a case study of land ownership and land use change in remote, rural Wallowa County, Oregon to explore how working landscapes are envisioned and enacted by various actors. The arrival of landowning amenity migrants, many of whom actively endorsed a working landscape vision, resulted in subtle but significant transformations in land use practices and altered opportunities for local producers. The working landscape ideal, while replete with tensions and contradictions, nevertheless functioned as an important alternative vision to the rural gentrification characteristic of other scenic Western environs.Keywords: rural gentrification, working landscape, discourse, land use, amenity migratio
The effect of pH on decomposition of Mylone (dazomet) and tridipam to fungitoxic methylisothiocyanate in wood
Full text linkMylone@ and tridipam are two solid chemicals that decompose to produce methylisothiocyanate (MIT), a highly effective wood fumigant. In this study, two techniques -- a rapid, test-tube method and small-scale, wood-block assay -- were used to determine the effect of the pH of various chemical buffers on the decomposition of Mylone@ and tridipam in Douglas-fir heartwood samples colonized by Poria carbonica. Both chemicals were sensitive to pH, and higher levels of MIT were produced as the pH of the buffers increased. In general, fungal survival was not affected 1 week after chemical treatment. Complete control of P. carbonica, however, resulted after 4 weeks of exposure to 50 mg Mylone@/block or 150 mg tridipam/block, when each chemical was combined with a pH-12 buffer. These results suggest that regulating fumigant treatments according to the degree of fungal attack can substantially improve the precision of decay control in wood maintenance programs.Keywords: wood decay, Mylone, tridipam, pH, methylisothiocyanate, Poria placenta, Poria carbonica, fumigants, Douglas-fir, buffers, utility pole
Asymmetry of price transmission within the French value chain of seafood products
Full text linkA recent study in agricultural products has brought out evidence of asymmetrical transmission of price changes according to the sign (positive or negative) of past variation. Interestingly, asymmetry was more commonplace for products with a lower elasticity of supply due to the perishable nature of products. A similar study based on TAR and M-TAR cointegration models is carried out on the French markets for fish products. In particular, it investigates the relation between the characteristics of supply (farmed or wild-caught species) and the results regarding asymmetry of price transmission along the supply chain of fresh products. Like in previous studies, it is expected that farming, by increasing the security of supply, shows less asymmetry than wild caught products. Results bring no evidence of asymmetric price transmission in any value chain, whatever the origin of the supply, farmed or wild. It is nevertheless found differences in terms of speed of adjustment and size of margin that can be interpreted as a consequence of the uncertainty in the conditions of supply.Keywords: cointegration, asymmetric price transmission, TAR and M-TAR models, International Seafood Trade: Rules Based Reform, Fisheries Economics, fish value chain