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...
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.
In the Pacific Northwest, USA, the extraordinarily low snowpacks of winters 2013–2014 and 2014– 2015 stressed regional water resources and the social environmental system. We introduce two new approaches to better understand how seasonal snow water storage during these two winters would compare to snow water storage under warmer climate...
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...
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...
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,...
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...
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...
This article provides a thorough meta-analysis of the anomaly detection problem. To accomplish this we first identify approaches to benchmarking anomaly detection algorithms across the literature and produce a large corpus of anomaly detection benchmarks that vary in their construction across several dimensions we deem important to real-world applications: (a)...
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...
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...
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...
This dataset contains results from direct numerical simulations of premixed, three-dimensional, turbulent hydrogen/air flames, using the multicomponent and mixture-averaged diffusion models. In particular, this dataset contains information about the enstrophy budget and flame structure. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the...
This data contains results from direct numerical simulations of premixed, two-dimensional unsteady and three-dimensional, turbulent hydrogen/air flames, using the multicomponent and mixture-averaged diffusion models. In particular, this dataset contains information about diffusion flux angles and magnitudes. We performed the simulations using the finite-difference code NGA; simulation details are described completely...
This data contains results from direct numerical simulations of premixed, three-dimensional, turbulent n-heptane/air flames, using the multicomponent and mixture-averaged diffusion models. In particular, this dataset contains information about diffusion flux angles and magnitudes. We performed the simulations using the finite-difference code NGA; simulation details are described completely in the associated...
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...
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...
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...
All necessary data files (including a README file) associated with the Master's Thesis titled: Contrasting Epiphytic and Ground Layer Macrolichen Communities along the Coast-to-inland Climatic Gradient in Oregon.
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 repository item contains the files needed to reproduce the results reported in the published work entitled "Runups of unusual size: rogueness and variability of swash" in the Journal of Geophysical Research. As described in the publication, the results described within it pertain to simulations of wave runup for various...
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...
1.) We investigated the potential of cross-scale interactions to affect the outcome of density reduction in a large-scale silvicultural experiment to better understand options for managing forests under climate change.
2.) We measured tree growth and intrinsic water-use efficiency (iWUE) based on stable carbon isotopes (d13C) to investigate impacts of...
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...
We characterized wildfire transmission and exposure within a matrix of large land tenures (federal, state, and private) surrounding 56 communities within a 3.3 million ha fire prone region of central Oregon US. Wildfire simulation and network analysis were used to quantify the exchange of fire among land tenures and communities...
Research data has gained wider acceptance as important scholarly products in and of themselves, and funding agencies, such as the National Science Foundation (NSF), have introduced requirements for Data Management Plans (DMPs) and data archiving. Accordingly, academic and research libraries are devoting significant consideration, effort, and resources toward expanding their...
The data represent 48-state USA weather and climate data (both site and gridded), biological phenology (developmental) models, combined with photoperiod response (diapause inducing sensitivity to short daylengths). The example data sets are specific to a single insect biological control organism (a leaf beetle introduced to control purple loosestrife, an invasive...
Dam removal is an important management tool for addressing aging infrastructure, public and structural safety, restoration of river connectivity for migratory organisms and recreation, and habitat quality. However, planning for dam removals is constrained by the difficulty of cost estimation. To our knowledge, published data on dam removal plans, total...
Dataset contains a 2015 partial re-measurement of the Blue Mountains Fire and Fire Surrogate study. 8 plots were measured from each of the 16 units, selected
randomly from all plots in each unit. Species are recorded using USDA plant codes, "UNKN" is unknown species. For fine fuels, 3 Brown's transects...
Data on green crabs collected and trapped from Makah Bay to Coos Bay in 2017.
Data included: Estuary, site, date, sex, carapace width, weight, molt state, estimated year class, missing limbs, collection method and collector.
Data on green crabs collected and trapped from Makah Bay to Coos Bay in 2018. Data included: Estuary, site, date, sex, carapace width, weight, molt state, estimated year class, missing limbs, collection method, collector and pheromone treatment.
European green crab, Carcinus maenas, trapped and collected in coastal Oregon and Washington coastal estuaries during the 2019. Data for individual crabs include: estuary, site, date of collection, sex, carapace width, weight, molt stage (color of abdomen), missing limbs, estimated year class, method of collection, and name of collector.
These data were obtained from GPS radio collared mule deer from 2015-2017 in the John Day Basin. The dataets includes location data for used vs available predictor variable information for time since fire, juniper canopy cover, NDVI, and vegetation community for winter, summer:migratory, summer:resident seasonal ranges. The datasets were used...
Crystal-rich (40~50 vol.%) intermediate lava has been the primary eruptive product of several recent hazardous eruptions: Mt. Pinatubo, Philippines (1991), Soufriere Hills, Montserrat (1995-present), and Unzen, Japan (1990-1995). Despite this association with such devastating eruptions, the formation, timing, and evacuation of such magma is not well understood: do such eruptions...
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...
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.
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.