Because studies of forestry effects on wetlands have been so infrequent in the Pacific Northwest, each section in this report drew heavily from studies of forestry impacts to streams and riparian zones. After assembly and synthesis, that information was extrapolated, mostly in the form of hypotheses, to the very different...
The purpose of this document (Framework) is to communicate some of the factors the Service is likely to consider in evaluating the efficacy of mitigation practices and programs in reducing threats to sage-grouse. The recommendations provided here are consistent with the information and conservation objectives provided in the 2013 Conservation...
The ascomycete Geosmithia morbida and the walnut twig beetle Pityophthorus juglandis are associated with thousand
cankers disease of Juglans (walnut) and Pterocarya (wingnut). The disease was first reported in the western United States
(USA) on several Juglans species, but has been found more recently in the eastern USA in the...
Phytophthora infestans, the causal agent of late blight disease, has been reported in North America since the mid-nineteenth century. In the United States the lack of or very limited sexual reproduction has resulted in largely clonal populations of P. infestans. In 2010 and 2011, but not in 2012 or 2013,...
Direct behavioral observations of multiple free-ranging animals over long periods of time and large geographic areas is prohibitively difficult. However, recent improvements in technology, such as Global Positioning System (GPS) collars equipped with motion-sensitive activity monitors, create the potential to remotely monitor animal behavior. Accelerometer-equipped activity monitors quantify animal motion...
The manufacturing processes of royal demolition explosive (RDX), or hexahydro-1,3,5-trinitro-1,3,5-triazine, have resulted in
serious water contamination. As a potential carcinogen, RDX can cause a broad range of harmful effects to humans and
animals. The ovine rumen is capable of rapid degradation of nitroaromatic compounds, including RDX. While ruminal RDX-degrading
bacteria...
Correction:
21 Jan 2015: The PLOS ONE Staff (2015) Correction: Separate Introns Gained within Short and Long Soluble Peridinin-Chlorophyll a-Protein Genes during Radiation of Symbiodinium (Dinophyceae) Clade A and B Lineages. PLOS ONE 10(1): e0117735. https://doi.org/10.1371/journal.pone.0117735
Temperature data received post mortem in 2008–13 from 15 of 36 juvenile Steller sea lions (Eumetopias jubatus) that had been surgically implanted in 2005–11 with dual life history transmitters (LHX tags) indicated that all 15 animals died by predation. In 3 of those 15 cases, at least 1 of the...
Ecological network models and analyses are recognized as valuable tools for understanding the dynamics and resiliency of
ecosystems, and for informing ecosystem-based approaches to management. However, few databases exist that can
provide the life history, demographic and species interaction information necessary to parameterize ecological network
models. Faced with the difficulty...
Long-distance exchange has long been recognized as a critical factor in the history of the ancient Near East, yet few studies have utilized robust analytical methods to trace the production and movement of specific goods at the interregional scale. Mundane goods such as pottery are particularly under-studied, and owing to...
Many marine populations exhibit high variability in the recruitment of young into the population. While environmental cycles and oceanography explain some patterns of replenishment, the role of other growth-related processes in influencing settlement and recruitment is less clear. Examination of a 65-mo. time series of recruitment of a common coral...
Global change and its associated temperature increase has directly or indirectly changed the distributions of hosts and pathogens, and has affected host immunity, pathogen virulence and growth rates. This has resulted in increased disease in natural plant and animal populations worldwide, including scleractinian corals. While the effects of temperature increase...
Biodiversity losses are occurring worldwide due to a combination of stressors. For example, by one estimate, 40% of amphibian species are vulnerable to extinction, and disease is one threat to amphibian populations. The emerging infectious disease chytridiomycosis, caused by the aquatic fungus Batrachochytrium dendrobatidis (Bd), is a contributor to amphibian...
Terrestrial lichen biomass is an important indicator of forage availability for caribou in northern regions, and can indicate vegetation shifts due to climate change, air pollution or changes in vascular plant community structure. Techniques for estimating lichen biomass have traditionally required destructive harvesting that is painstaking and impractical, so we...
Impact and relevance are valued by both plant pathologists and
the supporters of research and extension. Impact has been characterized
as the “So what?” of research results, and in applied research
in agriculture typically involves some change in human
behavior. This might involve, for instance, avoidance of broad
spectrum pesticides,...
We compiled a lake-water clarity database using publically available, citizen volunteer observations made between 1938 and 2012 across eight states in the Upper Midwest, USA. Our objectives were to determine (1) whether temporal trends in lake-water clarity existed across this large geographic area and (2) whether trends were related to...
Management of marine ecosystems increasingly demands comprehensive and quantitative assessments of ocean health, but lacks a tool to do so. We applied the recently developed Ocean Health Index to assess ocean health in the relatively data-rich US west coast region. The overall region scored 71 out of 100, with sub-regions...
Members of Gram-positive Actinobacteria cause economically important diseases to plants. Within the Rhodococcus genus,
some members can cause growth deformities and persist as pathogens on a wide range of host plants. The current model
predicts that phytopathogenic isolates require a cluster of three loci present on a linear plasmid, with...
New sources of genetic diversity must be incorporated into plant breeding programs if they are to continue increasing grain
yield and quality, and tolerance to abiotic and biotic stresses. Germplasm collections provide a source of genetic and
phenotypic diversity, but characterization of these resources is required to increase their utility...
Background
Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes...
BACKGROUND: Cranberries (Vaccinium macrocarpon Ait.) contain high levels of phytochemicals such as proanthocyanidins (PACs). These polymeric condensations of flavan-3-ol monomers are associated with health benefits. Our objective was to evaluate phytochemicals in fruit from Hawaiian cranberry relatives, V. reticulatum Sm. and V. calycinum Sm. Normal-phase HPLC coupled with fluorescence and...
Vitamin E improved liver histology in children and adults with NAFLD who participated in TONIC and PIVENS clinical trials, but with significant inter-individual variability in its efficacy. Cytochrome P450 4F2 (CYP4F2) is the major enzyme metabolizing Vit E, with two common genetic variants (V433M, rs2108622 and W12G, rs3093105) found to...
We report the sequence and characterization of the genomes of 21 isolates of Rhodococcus. Next generation sequencing technology was used to generate genome sequences. The reads for each genome were de novo assembled. The contigs were re-ordered, using the genome sequence of A44a as a reference. The program, Prokka, was...
We re-sequenced the Pseudoperonospora cubensis transcriptome to provide the first extensive transcriptome-wide survey of alternative splicing in an obligate biotrophic pathogen during host infection. The libraries from biological replicates of cucumber leaves infected with Ps. cubensis for 2, 3, 4, and 8 days post inoculation (dpi) were re-sequenced using 100-mer...
We hypothesized that changes in southeastern Bering Sea foraging conditions for black-legged kittiwakes (Rissa tridactyla)
have caused shifts in habitat use with direct implications for population trends. To test this, we compared at-sea
distribution, breeding performance, and nutritional stress of kittiwakes in three years (2008–2010) at two sites in the...
Powdery mildew of hop (Podosphaera macularis) may cause economic loss due to reductions in cone yield and quality. Quantitative estimates of crop damage from powdery mildew remain poorly characterized, especially the effect of late season disease management on crop yield and quality. Field studies in Washington State evaluated cone yield,...
A final report on activities related to a professional development activity titled, "Professional development in data curation". The Lundeen Award enabled me to attend the ICPSR workshop "Curating and Managing Research Data for Re-Use." The objective was to build professional capacity within OSUL&P that would empower us to achieve our...
Bighorn sheep (Ovis canadensis) were not known to live on Tiburón Island, the largest island in the Gulf of California and
Mexico, prior to the surprisingly successful introduction of 20 individuals as a conservation measure in 1975. Today, a stable
island population of ~500 sheep supports limited big game hunting...
Background: Triticum monococcum (2n) is a close ancestor of T. urartu, the A-genome progenitor of cultivated hexaploid wheat, and is therefore a useful model for the study of components regulating photomorphogenesis in diploid wheat. In order to develop genetic and genomic resources for such a study, we constructed genome-wide transcriptomes...
Matlab code is included for detecting and tracking acoustic scattering layers from processed Echoview data. Acoustic scattering layers are ubiquitous, horizontally extensive aggregations of both vertebrate and invertebrate organisms that play key roles in oceanic ecosystems. However, currently there are no conventions or widely adaptable automatic methods for identifying these...
Nematodes within the Xiphinema americanum species complex are economically important because they vector nepoviruses which cause considerable damage to a variety of agricultural crops. The taxonomy of X. americanum species complex is controversial, with the number of putative species being the subject of debate. Accurate phylogenetic knowledge of this group...
Vibrio vulnificus and V. parahaemolyticus in the estuarine-marine environment are of human health significance and may be increasing in pathogenicity and abundance. Vibrio illness originating from dermal contact with Vibrio laden waters or through ingestion of seafood originating from such waters can cause deleterious health effects, particularly if the strains...
Human activity has been shown to considerably affect the spread of dangerous pests and pathogens worldwide. Therefore, strict regulations of international trade exist for particularly harmful pathogenic organisms. Phytophthora plurivora, which is not subject to regulations, is a plant pathogen frequently found on a broad range of host species, both...
Rapamycin was found to increase (11% to 16%) the lifespan of male and female C57BL/6J mice most likely by reducing the increase in the hazard for mortality (i.e., the rate of aging) term in the Gompertz mortality analysis. To identify the pathways that could be responsible for rapamycin's longevity effect,...
Ungulates exert a strong influence on the composition and diversity of vegetation communities. However, little is known about how ungulate browsing pressure interacts with episodic disturbances such as fire and stand thinning. We assessed shrub responses to variable browsing pressure by cattle and elk in fuels treated (mechanical removal of...
Condors and vultures are distinct from most other terrestrial birds because they use extensive soaring flight for their daily movements. Therefore, assessing resource selection by these avian scavengers requires quantifying the availability of terrestrial-based habitats, as well as meteorological variables that influence atmospheric conditions necessary for soaring. In this study,...
Virus-infected plants accumulate abundant, 21–24 nucleotide viral siRNAs which are generated by the evolutionary conserved RNA interference (RNAi) machinery that regulates gene expression and defends against invasive nucleic acids. Here we show that, similar to RNA viruses, the entire genome sequences of DNA viruses are densely covered with siRNAs in...
Transcription factor (TF) genes were modified endogenously to include epitope tags for identification of TF protein binding sites by Chromatin Immunoprecipitation (ChIP), followed by high throughput sequencing. We used RNA-sequencing in carbon sources of sucrose, butyrate, and oleate in far-1, far-2, and a double far-1; far-2 mutant to find transcripts...