Using spatial autocorrelation analysis, we
examined the within-population genetic structure of
Rhizopogon vinicolor and R. vesiculosus, two hypogeous
ectomycorrhizal (EM) species that are sympatric
sister taxa known to differ in their clonal structure.
We collected 121 sporocarps and 482 tuberculate EM
of both species from a 20 ha forest stand...
Introduction: Biotic soil crust communities contribute valuable ecosystem services and biodiversity in steppe ecosystems. The uncommon crust lichens Acarospora schleicheri, Fuscopannaria cyanolepra, Rhizocarpon diploschistidina, and Texosporium sancti-jacobi are associated with fine-textured soils along rivers of the Columbia Basin. A. schleicheri and R. diploschistidina indicate late-successional habitat and may serve as...
Background: Next-generation sequencing and 'omics' platforms are used extensively in plant biology research to unravel new genomes and study their interactions with abiotic and biotic agents in the growth environment. Despite the availability of a large and growing number of genomic data sets, there are only limited resources providing highly-curated...
Explaining restoration failure can be as important as touting success. We used a series of studies to understand the failure of techniques commonly used to restore wetland prairies in the Willamette Valley of western Oregon. Burning, fallowing, and solarization (covering tilled plots with plastic sheeting to heat the soil) had...
Plant growth stages are identified as distinct morphological landmarks in a continuous developmental process. The terms
describing these developmental stages record the morphological appearance of the plant at a specific point in its life cycle. The
widely differing morphology of plant species consequently gave rise to heterogeneous vocabularies describing growth...
The improvement of the agricultural and wine-making qualities of the grapevine (Vitis vinifera) is hampered by adherence to traditional varieties, the recalcitrance of this plant to genetic modifications, and public resistance to genetically modified organism (GMO) technologies. To address these challenges, we developed an RNA virus-based vector for the introduction...
Faced with landscapes degraded by fire suppression, logging, and grazing, land managers in the interior western US are attempting to restore habitat structure and function. In southwest Oregon, landscape-scale fuels treatments are being implemented with goals including recreating historic vegetation structure, despite poor understanding of the nature of the landscape...
Pseudomonas syringae is a phylogenetically diverse species of Gram-negative bacterial plant pathogens responsible for crop diseases around the world. The HrpL sigma factor drives expression of the major P. syringae virulence regulon. HrpL controls expression of the genes encoding the structural and functional components of the type III secretion system...
Antibiotics are essential for control of bacterial diseases of plants, especially fire blight of pear and apple and bacterial spot of peach. Streptomycin is used in several countries; the use of oxytetracycline, oxolinic acid and gentamicin is limited to only a few countries. Springtime antibiotic sprays suppress pathogen growth on...
Background: Recent mapping of eukaryotic transcriptomes and spliceomes using massively parallel RNA sequencing (RNA-seq) has revealed that the extent of alternative splicing has been considerably underestimated. Evidence also suggests that many pre-mRNAs undergo unproductive alternative splicing resulting in incorporation of in-frame premature termination codons (PTCs). The destinies and potential functions...
Raspberry latent virus (RpLV) is a newly characterized reovirus found in commercial raspberry fields in the Pacific Northwest (PNW). Thus far, all members of the plant reoviruses are transmitted in a replicative, persistent manner by several species of leafhoppers or planthoppers. After several failed attempts to transmit RpLV using leafhoppers,...
Questions: Are traits related to the performance of plant species in restoration? Are the relationships between traits and performance consistent across the functional groups of annual forbs, perennial forbs, and grasses? Do the relationships between traits and performance depend on neighboring functional groups? Location: A former agricultural field, being restored...
Disease predictive systems are intended to be management aids. With a few exceptions, these systems typically do not have direct sustained use by growers. Rather, their impact is mostly pedagogic and indirect, improving recommendations from farm advisers and shaping management concepts. The degree to which a system is consulted depends...
The Pseudomonas aeruginosa antimetabolite L-2-amino-4-methoxy-trans-3-butenoic acid (AMB) shares biological activities with 4-formylaminooxyvinylglycine, a related molecule produced by Pseudomonas fluorescens WH6. We found that culture filtrates of a P.aeruginosa strain overproducing AMB weakly interfered with seed germination of the grassy weed Poa annua and strongly inhibited growth of Erwinia amylovora, the...
Formal description of plant phenotypes and standardized annotation of gene expression and protein localization data require
uniform terminology that accurately describes plant anatomy and morphology. This facilitates cross species comparative
studies and quantitative comparison of phenotypes and expression patterns. A major drawback is variable terminology that is
used to describe...
The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort
among model plant genome databases and plant
researchers that aims to create, maintain and
facilitate the use of a controlled vocabulary
(ontology) for plants. The ontology allows users to
ascribe attributes of plant structure (anatomy and
morphology) and developmental stages...
The 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...
Plants are constantly exposed to a large and diverse array of microbes; however, most plants are immune to the majority of potential invaders and susceptible to only a small subset of pathogens. The cytoskeleton comprises a dynamic intracellular framework that responds rapidly to biotic stresses and supports numerous fundamental cellular...
Understanding the systematics and evolution of clavicipitoid fungi has been greatly aided by the application of molecular phylogenetics. They are now classified in three families, largely driven by reevaluation of the morphologically and ecologically diverse genus Cordyceps. Although reevaluation of morphological features of both sexual and asexual states were often...
Background: Large molecular sequence databases are fundamental resources for modern
bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often
advantageous to maintain smaller sequence databases. However, this is usually not an easy task for
the average bench scientist.
Results: We present the Personal Sequence Database (PSD),...