Plasmid transformation of chlamydiae has created new opportunities to investigate host–microbe interactions during chlamydial infections; however, there are still limitations. Plasmid transformation requires a replicon derived from the native Chlamydia plasmid, and these transformations are species-specific. We explored the utility of a broad host-range plasmid, pBBR1MCS-4, to transform chlamydiae, with...
Published December 1909. 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/catalog
Forest surveys provide critical information for many diverse interests. Data are often collected from samples, and from these samples, maps of resources and estimates of aerial totals or averages are required. In this paper, two approaches for mapping and estimating totals; the spatial linear model (SLM) and k-NN (k-Nearest Neighbor)...
This dataset was used to determine the attenuation of an audio signal by reticulated foam samples that span the natural range of intrinsic permeability for seasonal snow. Data are audio measurements acquired on a two-channel oscilloscope.
The distribution and range of lesser prairie-chicken (Tympanuchus pallidicinctus) has been reduced by >90% since European settlement of the Great Plains of North America. Currently, lesser prairie-chickens occupy 3 general vegetation communities: sand sagebrush (Artemisia filifolia), sand shinnery oak (Quercus havardii), and mixed-grass prairies juxtaposed with Conservation Reserve Program grasslands....
The diverse predatory rockfishes (Sebastes spp.) support extensive commercial fisheries in the northeastern Pacific. Although 106 species of Sebastes are considered valid, many of the ecological, geographical, and morphological boundaries separating them lack clarity. We clarify one such boundary by separating the blue rockfish Sebastes mystinus (Jordan and Gilbert, 1881)...
Western Atlantic synodontid species were studied as part of an ongoing effort to reanalyze Caribbean shorefish diversity. A neighbor-joining tree constructed from cytochrome c oxidase I (COI) data revealed 2 highly divergent genetic lineages within both Synodus intermedius (Agassiz, 1829) (Sand Diver) and S. foetens (Linnaeus, 1766) (Inshore Lizardfish). A...
Published March 1925. 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/catalog
Published September 1926. 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/catalog
Patterns of seasonal abundance of harbor seals at Netarts and Tillamook Bays, Oregon, were documented by recording numbers of seals hauling out on tidally exposed sand flats in both bays. Harbor seal abundance at Tillamook Bay peaked during pupping (May-June) and molting (August) periods, while peak abundance at Netarts Bay...
In Kentucky bluegrass (Poa pratensis), Claviceps purpurea, the causal agent of ergot, typically releases ascospores during the early-morning hours, between about midnight and 10:00 A.M., corresponding to time of flowering, when the unfertilized ovaries are most susceptible to infection. During aeromycology studies of C. purpurea in perennial ryegrass (Lolium perenne)...
During July 1970, albacore boats trolling surface jigs (jig boats) had record catches in an area off the mouth of the Columbia River. The jig fishery declined suddenly in late July and was poor throughout the remainder of the summer. No obvious oceanographic changes were correlated with these drastic changes...
Published December 1910. 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/catalog
To investigate the effects of logging, three small watersheds in the Alsea River basin on the west slope of the Oregon Coast Range were selected for study. This was an interdisciplinary investigation to evaluate the influence of specific logging methods on stream regimen and on aquatic resources. The study plan...
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,...
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...
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...
Published 1890. 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/catalog
Covers the period from March 1, 1893-November 30, 1894. Discusses fisheries and game legislation and enforcement, dams, hatcheries, financial reporting and organizational structure, and fisheries statistics.
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...
Published June 1927. 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/catalog
Motivation:
Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of...
Background: Arsenic is an immunotoxicant. Clinical reports observe the reactivation of varicella zoster virus (VZV) in people who have recovered from arsenic poisoning and in patients with acute promyelocytic leukemia that have been treated with arsenic trioxide. Objective: We evaluated the association between arsenic and the seroprevalence of VZV IgG...
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...
A recent identification of the two-component aggregation pheromone of the invasive stink bug species, Halyomorpha halys (Stal), in association with a synergist, has greatly improved the ability to accurately monitor the seasonal abundance and distribution of this destructive pest. We evaluated the attraction of H. halys to black pyramid traps...
This dataset accompanies the manuscript Unintended consequences of selective water withdrawals from reservoirs alter downstream macroinvertebrate communities in Water Resources Research.
Benthic macroinvertebrates were collected from samples taken annually during the first two weeks of August from 2002-2007 and again in 2017 at six sites in the South Fork McKenzie...
We form a new data set of fields of sea level anomalies by combining gridded daily fields derived from altimeter data with coastal tide gauge data. Within approximately 50-80 km of the coast, the altimeter data are discarded and replaced by a linear interpolation between the tide gauge and remaining...
We form a new data set of fields of sea level anomalies by combining gridded daily fields derived from altimeter data with coastal tide gauge data. Within approximately 50-80 km of the coast, the altimeter data are discarded and replaced by a linear interpolation between the tide gauge and remaining...
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...
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...
Dual-axis accelerometer global positioning system collars can be used to remotely record the activity level and behavior of free-ranging animals, but inter- and intraspecific variations in motion among behaviors necessitate calibration for each species of interest. To date, little work has been done to determine the best duration for sampling...
There will be winners and losers as climate change alters the habitats of polar organisms. For an Adelie penguin (Pygoscelis adeliae) colony on Beaufort Island (Beaufort), part of a cluster of colonies in the southern Ross Sea, we report a recent population increase in response to increased nesting habitat as...
The genomes of five Cochliobolus heterostrophus strains, two Cochliobolus sativus strains, three additional Cochliobolus species (Cochliobolus victoriae, Cochliobolus carbonum, Cochliobolus miyabeanus), and closely related Setosphaeria turcica were sequenced at the Joint Genome Institute (JGI). The datasets were used to identify SNPs between strains and species, unique genomic regions, core secondary...
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades,...
We provide here a comparative genome analysis of ten strains within the Pseudomonas fluorescens group including seven new genomic sequences. These strains exhibit a diverse spectrum of traits involved in biological control and other multitrophic interactions with plants, microbes, and insects. Multilocus sequence analysis placed the strains in three sub-clades,...
Movement in an important component of an animal’s life cycle when it relies on both aquatic and terrestrial habitats. When multiple species overlap in the use of these habitats, they rely on other methods to reduce competition for shared resources. This dataset measured the jumping performance and movement behavior of...
Submersible belt-transect surveys along a rocky bottom were combined with acoustic surveys of the water column to estimate depth distribution and density of fishes at Stonewall Bank, Oregon in the northeastern Pacific Ocean from September through October 1991. The objectives of the study were to determine the proportion of fish...
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,...
The author reviewed the professional literature concerning elementary school aged children of alcoholics (ECOAs). The literature suggests that ECOAs encounter problems with cognitive, behavioral, and familial functioning. The implications of ECOA research for counseling practice were discussed.
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,...
Land-use change around protected areas can reduce their effective size and limit their ability to conserve biodiversity
because land-use change alters ecological processes and the ability of organisms to move freely among protected areas.
The goal of our analysis was to inform conservation planning efforts for a nationwide network of...
This dataset is based on quantitative PCR (qPCR) output. Output from all qPCR was compiled in this dataset and kept as the original. Information about sampling time, id, concentration, sites and a conversion of the quantity in femtograms were added as complement to the qPCR output to facilitate data analysis
This dataset contains data layers used and produced by a fuzzy logic model for biomass loss risk under projected climate change in Oregon and Washington west of the Cascade Mountains crest.
This dataset supports a research project and paper where we define criteria for assessing the effectiveness of data sharing, under the assumption that the goal of data sharing is to make the data usable, with minimal effort, to the new user. We take the position that the bar should be...
Ampelisca eschrichtii are among the most important prey of the Western North Pacific gray whales, Eschrichtius robustus. The largest and densest known populations of this amphipod occur in the gray whale’s Offshore feeding area on the Northeastern Sakhalin Island Shelf. The remote location, ice cover and stormy weather at the...
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...
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...
The fungus Fusarium fujikuroi causes "bakanae" disease of rice due to its ability to produce gibberellins (GAs), but it is also known for producing harmful mycotoxins. However, the genetic capacity for the whole arsenal of natural compounds and their role in the fungus' interaction with rice remained unknown. Here, we...
A number of researchers have attempted to estimate salmonid smolt survival during outmigration through an estuary. However, it is currently unclear how the design of such studies influences the accuracy and precision of survival estimates. In this simulation study we consider four patterns of smolt survival probability in the estuary,...
Correction
21 Jun 2012: Verde I, Bassil N, Scalabrin S, Gilmore B, Lawley CT, et al. (2012) Correction: Development and Evaluation of a 9K SNP Array for Peach by Internationally Coordinated SNP Detection and Validation in Breeding Germplasm. PLOS ONE 7(6): 10.1371/annotation/33f1ba92-c304-4757-91aa-555de64a0768.
To detect and avoid illegal logging of valuable tree species, identification methods for the origin of timber are necessary. We used next-generation sequencing to identify chloroplast genome regions that differentiate the origin of white oaks from the three continents; Asia, Europe, and North America. By using the chloroplast genome of...
Knowledge of processes leading to crop damage is central to devising rational approaches to disease management. Multiple experiments established that infection of hop cones by Podosphaera macularis was most severe if inoculation occurred within 15 to 21 days after bloom. This period of infection was associated with the most pronounced...
We studied avian development in 49 species of temperate and 153 species of tropical New World passerine birds to determine how growth rates, and incubation and nestling periods, varied in relation to other life-history traits. We collected growth data and generated unbiased mass and tarsus growth rate estimates (mass n...
Sexually size-dimorphic species must show some difference between the sexes in growth rate and/or length of growing period. Such differences in growth parameters can cause the sexes to be impacted by environmental variability in different ways, and understanding these differences allows a better understanding of patterns in productivity between individuals...
This data contains results from direct numerical simulations of three-dimensional, premixed, hydrogen/air flames, using the mixture-averaged diffusion model. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated article.
This data contains results from direct numerical simulations of three-dimensional, premixed, hydrogen/air flames, using the multicomponent diffusion model. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated article.
Published March 1925. 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/catalog
A steam distillation extraction kinetics experiment was conducted to estimate essential oil yield, composition, antimalarial, and antioxidant capacity of cumin (Cuminum cyminum L.) seed (fruits). Furthermore, regression models were developed to predict essential oil yield and composition for a given duration of the steam distillation time (DT). Ten DT durations...
Host resistance, both quantitative and qualitative, is the preferred long-term approach for disease management in many pathosystems, including powdery mildew of hop (Podosphaera macularis). In 2012, an epidemic of powdery mildew occurred in Washington and Idaho on previously resistant cultivars whose resistance was putatively based on the gene designated R6....
Correction
5 Mar 2013: Ohm RA, Feau N, Henrissat B, Schoch CL, Horwitz BA, et al. (2013) Correction: Diverse Lifestyles and Strategies of Plant Pathogenesis Encoded in the Genomes of Eighteen Dothideomycetes Fungi. PLOS Pathogens 9(3): 10.1371/annotation/fcca88ac-d684-46e0-a483-62af67e777bd
Stream-dwelling species in the U.S. southern Appalachian Mountains region are particularly vulnerable to climate change and acidification. The objectives of this study were to quantify the spatial extent of contemporary suitable habitat for acid- and thermally sensitive aquatic species and to forecast future habitat loss resulting from expected temperature increases...
The quantification and description of sea surface temperature (SST) is critically important because it can influence the distribution, migration, and invasion of marine species; furthermore, SSTs are expected to be affected by climate change. To better understand present temperature regimes, we assembled a 29-year nearshore time series of mean monthly...
Fusarium crown rot (FCR) is one of the most widespread root and
crown diseases of wheat in the Pacific Northwest (PNW) of the United
States. Our objectives were to characterize crown rot severity and
distribution throughout the PNW by conducting a survey of 210 fields
covering the diverse dryland wheat-producing...
The HIV pandemic continues to impose enormous morbidity, mortality and economic burdens across the globe. Simultaneously, innovations in antiretroviral therapy, diagnostic approaches and vaccine development are providing novel tools for treatment-as-prevention and prophylaxis. We developed a mathematical model to evaluate the added benefit of an HIV vaccine in the context...
Engineered log jams (ELJs) are commonly implemented in rivers to stabilize streambanks and diversify fish habitat, but few studies have verified the hydraulic benefits of ELJs by assessing their effects on the flow field. This field and modeling study assessed the effects of an ELJ on various characteristics of the...
The Bering Sea and Gulf of Alaska support a number of commercially important flatfish fisheries. These high latitude ecosystems are predicted to be most immediately impacted by ongoing ocean acidification, but the range of responses by commercial fishery species has yet to be fully explored. In this study, we examined...
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...
Recent attention has focused on the high rates of annual carbon sequestration in vegetated coastal ecosystems—marshes, mangroves, and seagrasses—that may be lost with habitat destruction (‘conversion’). Relatively unappreciated, however, is that conversion of these coastal ecosystems also impacts very large pools of previously-sequestered carbon. Residing mostly in sediments, this ‘blue...
Cymbopogon flexuosus, lemongrass, and C. martinii, palmarosa, are perennial grasses grown to produce essential oils for the fragrance industry. The objectives of this study were (1) to evaluate biomass and oil yields as a function of nitrogen and sulfur fertilization, and (2) to characterize their utility for lignocellulosic ethanol compared...
Correction
23 Dec 2015: The PLOS ONE Staff (2015) Correction: Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders. PLOS ONE 10(12): e0145899. https://doi.org/10.1371/journal.pone.0145899
Climate change is expected to change the distribution of species. For long-lived, sessile
species such as trees, tracking the warming climate depends on seedling colonization of
newly favorable areas. We compare the distribution of seedlings and mature trees for all but
the rarest tree species in California, Oregon and Washington,...