The epiphytic lichen Letharia vulpina has been commonly sampled in-situ for nitrogen (N) deposition biomonitoring studies but has never before been transplanted for this purpose. In the high-elevation wilderness areas of southern California Letharia vulpina is generally uncommon, making in-situ sampling difficult. In this study, we compared thallus N accumulation...
The role of small secreted peptides in plant defense responses to viruses has been seldom investigated. Here, we report a role for potato (Solanum tuberosum) PIP1, a gene predicted to encode a member of the PAMP-induced peptide (PIP) family, in the response of potato to potato virus Y infection (PVY)....
The objectives of this study are to isolate and characterize pathogenic agrobacteria that cause crown gall in grapevines and test hot water dips as a method for eradicating the infectious bacteria . Crown gall is commonly found among Oregon vineyards and the causative agent, Agrobacterium vitis, is known to be...
The sweet potato is one of the world’s most widely consumed crops, yet its evolutionary history is poorly understood. In this paper, we present a comprehensive phylogenetic study of all species closely related to the sweet potato and address several questions pertaining to the sweet potato that remained unanswered. Our...
Phylogenetics benefits from using a large number of putatively independent nuclear loci and their combination with other sources of information, such as the plastid and mitochondrial genomes. To facilitate the selection of orthologous low‐copy nuclear (LCN) loci for phylogenetics in nonmodel organisms, we created an automated and interactive script to...
Micronutrient deficiency, also known as the hidden hunger, affects over two billion people worldwide. Potato is the third most consumed food crops in the world, and is therefore a fundamental element of food security for millions of people. Increasing the amount of micronutrients in food crop could help alleviate worldwide...
The dataset here is used as a document file for presenting supplementary videos in the dissertation Tao, K. (2018). Investigating protein-lipid-membrane interactions in Plant Cells using Bimolecular Fluorescence Complementation (Doctoral dissertation).
Keywords: Protein, Lipid, Membrane, Plant Cells, Fluorescent Imaging
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...
Question: Most results of restoration efforts are species-specific and/or site-specific and therefore are not general enough to be easily applied to other species and other sites. Our research addresses the issue of species-specific results by investigating the feasibility of using plant traits instead of taxonomic species to characterize species responses...
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...
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...
Phytophthora infestans, the cause of the devastating late blight disease of potato and tomato, exhibits a clonal reproductive lifestyle in North America. Phenotypes such as fungicide sensitivity and host preference are conserved among individuals within clonal lineages, while substantial phenotypic differences can exist between lineages. Whole P. infestans genomes were...
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....
This is the publisher’s final pdf. The published article is copyrighted by the author(s) and published by the Genetics Society of America. The published article can be found at: https://doi.org/10.1534/g3.116.027045
Mountain environments are currently among the ecosystems least invaded by non-native species; however, mountains are increasingly under threat of non-native plant invasion. The slow pace of exotic plant invasions in mountain ecosystems is likely due to a combination of low anthropogenic disturbances, low propagule supply, and extreme/steep environmental gradients. The...
Forest health issues are on the rise in the United States, resulting from introduction of alien pests and diseases, coupled with abiotic stresses related to climate change. Increasingly, forest scientists are finding genetic/genomic resources valuable in addressing forest health issues. For a set of ten ecologically and economically important native...
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize...
RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data...
Nitrogen-fixing lichens (cyanolichens) are an important source of nitrogen (N) in Pacific Northwest forests, but limitation of lichen growth by elements essential for N fixation is poorly understood. To investigate how nutrient limitation may affect cyanolichen growth rates, we fertilized a tripartite cyanobacterial lichen (Lobaria pulmonaria) and a green algal...
Optimum timing and use of fungicides for disease control are improved by an understanding of the characteristics of fungicide physical mode of action. Greenhouse and field experiments were conducted to quantify and model the duration of pre- and postinfection activity of fungicides most commonly used for control of hop downy...
Results of 28 field trials conducted over a 12-year period investigating management of hop powdery mildew caused by Podosphaera macularis were quantitatively summarized by meta-analysis to compare product efficacy and use patterns by mode of action as defined by Fungicide Resistance Action Committee (FRAC) groups. Availability of original observations enabled...
The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
In eukaryotes, ARGONAUTE proteins (AGOs) associate with microRNAs (miRNAs), short interfering RNAs (siRNAs), and other classes of small RNAs to regulate target RNA or target loci. Viral infection in plants induces a potent and highly specific antiviral RNA silencing response characterized by the formation of virus-derived siRNAs. Arabidopsis thaliana has...
Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across...
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,...
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
Viruses are obligatory parasites that depend on host cellular factors for their replication as well as for their local and systemic movement to establish infection. Although myosin motors are thought to contribute to plant virus infection, their exact roles in the specific infection steps have not been addressed. Here we...
Primula sect. Parryi comprises five species endemic to western North America: P. parryi, P. angustifolia, P. rusbyi, P. capillaris, and P. cusickiana with four varieties. This section, derived from a clade with representatives in Asia and Europe, exemplifies a phytogeographic pattern in which a widespread species is accompanied by multiple...
Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms...
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,...
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...
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...
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 Arabidopsis Information Portal (AIP), a resource expected to provide access to all community data and combine outputs into
a single user-friendly interface, has emerged from community discussions over the last 23 months. These discussions began
during two closely linked workshops in early 2010 that established the International Arabidopsis Informatics...
The Gene Ontology (GO) Consortium (http://www.geneontology.org) (GOC) continues to develop,
maintain and use a set of structured, controlled
vocabularies for the annotation of genes, gene
products and sequences. The GO ontologies
are expanding both in content and in structure.
Several new relationship types have been introduced
and used, along with...
Gramene (http://www.gramene.org/) is a comparative genome database for cereal crops
and a community resource for rice. We are populating and curating Gramene with
annotated rice (Oryza sativa) genomic sequence data and associated biological information
including molecular markers, mutants, phenotypes, polymorphisms and Quantitative Trait
Loci (QTL). In order to support queries...
The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative
effort among several plant databases and experts in plant systematics, botany
and genomics. A primary goal of the POC is to develop simple yet robust
and extensible controlled vocabularies that accurately reflect the biology of plant
structures and developmental stages. These...
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 Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the
application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity
is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the...
Gramene (www.gramene.org) is a curated resource
for genetic, genomic and comparative genomics
data for the major crop species, including rice,
maize, wheat and many other plant (mainly grass)
species. Gramene is an open-source project.
All data and software are freely downloadable
through the ftp site (ftp.gramene.org/pub/gramene)
and available for use...
Gramene (http://www.gramene.org) is a comparative genome mapping database for grasses and a community resource for rice. Rice, in addition to being an economically important crop, is also a model monocot for understanding other agronomically important grass genomes. Gramene replaces the existing AceDB database ‘RiceGenes’ with a relational database based on...
Rice, maize, sorghum, wheat, barley and the other
major crop grasses from the family Poaceae
(Gramineae) are mankind’s most important source
of calories and contribute tens of billions of dollars
annually to the world economy (FAO 1999, http://www.fao.org; USDA 1997, http://www.usda.gov).
Continued improvement of Poaceae crops is necessary
in order...
Gramene is a comparative information resource for plants that integrates data across diverse data domains. In this article,
we describe the development of a quantitative trait loci (QTL) database and illustrate how it can be used to facilitate
both the forward and reverse genetics research. The QTL database contains the...
BACKGROUND: Circadian clocks provide an adaptive advantage through anticipation of daily and seasonal environmental
changes. In plants, the central clock oscillator is regulated by several interlocking feedback loops. It was shown that a
substantial proportion of the Arabidopsis genome cycles with phases of peak expression covering the entire day.
Synchronized...
Now in its 10th year, the Gramene database (http://www.gramene.org) has grown from its primary focus on rice, the first fully-sequenced grass genome, to become a resource for major model and crop plants including Arabidopsis, Brachypodium, maize, sorghum, poplar and grape in addition to several species of rice. Gramene began with...
Plants possess two myosin classes, VIII and XI. The myosins XI are implicated in organelle transport, filamentous actin
organization, and cell and plant growth. Due to the large size of myosin gene families, knowledge of these molecular motors
remains patchy. Using deep transcriptome sequencing and bioinformatics, we systematically investigated myosin...
PREMISE OF THE STUDY: We report the de novo assembly and characterization of the transcriptomes of Brachypodium sylvaticum
(slender false-brome) accessions from native populations of Spain and Greece, and an invasive population west of Corvallis,
Oregon, USA.
METHODS AND RESULTS: More than 350 million sequence reads from the mRNA libraries...
Repetitive sequences present a challenge for genome sequence assembly, and highly similar segmental duplications may disappear from assembled genome sequences. Having found a surprising lack of observable phenotypic deviations and non-Mendelian segregation in Arabidopsis thaliana mutants in SEC10, a gene encoding a core subunit of the exocyst tethering complex, we...
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...
Agricultural land management, such as fertilization, liming, and tillage affects soil properties, including pH, organic matter content, nitrification rates, and the microbial community. Three different study sites were used to identify microorganisms that correlate with agricultural land use and to determine which factors regulate the relative abundance of the microbial...
Grapevine leafroll disease (GLD) is one of the most important grapevine viral diseases affecting grapevines worldwide. The impact on vine health, crop yield, and quality is difficult to assess due to a high number of variables, but significant economic losses are consistently reported over the lifespan of a vineyard if...
Important progress in understanding replication, interactions with host plants, and evolution of closteroviruses enabled engineering of several vectors for gene expression and virus-induced gene silencing. Due to the broad host range of closteroviruses, these vectors expanded vector applicability to include important woody plants such as citrus and grapevine. Furthermore, large...
Submarine volcanic eruptions can result in both real and apparent changes in marine algal communities, e.g., increases in phytoplankton biomass and/or growth rates that can cover thousands of square kilometers. Satellite ocean color monitoring detects these changes as increases in chlorophyll and particulate backscattering. Detailed, high resolution analysis is needed...
In eukaryotes, RNA silencing pathways utilize 20-30-nucleotide small RNAs to regulate gene expression, specify and maintain chromatin structure, and repress viruses and mobile genetic elements. RNA silencing was likely present in the common ancestor of modern eukaryotes, but most research has focused on plant and animal RNA silencing systems. Phytophthora...
Viruses and/or virus-like selfish elements are associated with all cellular life forms and are the most abundant biological entities on Earth, with the number of virus particles in many environments exceeding the number of cells by one to two orders of magnitude. The genetic diversity of viruses is commensurately enormous...
Beauveria sinensis sp. nov. was isolated from a larva of Geometridae (Lepidoptera) collected from Tiantangzhai, Anhui province, China. It is characterized by elongated ellipsoidal to cylindrical conidia, solitary conidiogenous cells that are cylindrical or with slightly swollen bases, white to pale pink colony in culture, and small mycelial pellets consisting...
Global ocean phytoplankton biomass (C-phyto) and total particulate organic carbon (POC) stocks have largely been characterized from space using passive ocean color measurements. A space-based light detection and ranging (lidar) system can provide valuable complementary observations for C-phyto and POC assessments, with benefits including day-night sampling, observations through absorbing aerosols...
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...
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...
To characterize the mechanism through which myosin XI-K attaches to its principal endomembrane cargo, a yeast two-hybrid library of Arabidopsis thaliana cDNAs was screened using the myosin cargo binding domain as bait. This screen identified two previously uncharacterized transmembrane proteins (hereinafter myosin binding proteins or MyoB1/2) that share a myosin...
Spatial variation of available food resources can be difficult to accurately quantify for wide ranging organisms
at landscape scales. Lichens with usnic acid, a yellowish pigment, constitute a large portion of caribou winter
diet across much of their range. We take a new approach of modeling lichen abundances by capitalizing...
The ascomycete fungus Tolypocladium inflatum, a pathogen of beetle larvae, is best known as the producer of the immunosuppressant drug cyclosporin. The draft genome of T. inflatum strain NRRL 8044 (ATCC 34921), the isolate from which cyclosporin was first isolated, is presented along with comparative analyses of the biosynthesis of...
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...
Although Oregon white oak (Quercus garryana) woodlands are a characteristic landscape component in southwestern Oregon, little is known about their current or historical stand structures. Meanwhile, fuel reduction thinning treatments that change stand structures in non-coniferous communities are ongoing and widespread on public lands in this region; some of these...
Heterodera avenae is widely distributed in areas where most cereal crops are produced in Algeria. However, the virulence of the Algerian populations of this nematode on individual cereal species and cultivars has not been well documented. The virulence of H. avenae populations from Tiaret and from Oued Smar were tested...
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...
Conjugative plasmids are known to facilitate the acquisition and dispersal of genes contributing to the fitness of Pseudomonas spp. Here, we report the characterization of pA506, the 57-kb conjugative plasmid of Pseudomonas fluorescens A506, a plant epiphyte used in the United States for the biological control of fire blight disease...
A framework for understanding the synthesis and catalysis of metabolites and other biochemicals by proteins is crucial for unraveling the physiology of cells. To create such a framework for Zea mays L. subsp. mays (maize), we developed MaizeCyc, a metabolic network of enzyme catalysts, proteins, carbohydrates, lipids, amino acids, secondary...
Satellite measurements allow global assessments of phytoplankton concentrations and, from observed temporal changes in biomass, direct access to net biomass accumulation rates (r). For the subarctic Atlantic basin, analysis of annual cycles in r reveals that initiation of the annual blooming phase does not occur in spring after stratification surpasses...
Raman scattering can be a significant contributor to the emergent radiance spectrum from the surface ocean. Here, we present an analytical approach to directly estimate the Raman contribution to remote sensing reflectance, and evaluate its effects on optical properties estimated from two common semi analytical inversion models. For application of...
Two diametric paradigms have been proposed to model the molecular co-evolution of microbial mutualists and their eukaryotic hosts. In one, mutualist and host exhibit an antagonistic arms race and each partner evolves rapidly to maximize their own fitness from the interaction at potential expense of the other. In the opposing...
Field surveys in 2006 confirmed that the
exotic rust fungus Phragmidium violaceum was widespread
on Rubus armeniacus and Rubus laciniatus in
the Pacific Northwest of the USA. The origin and
dispersal pattern of this obligate biotrophic pathogen in
the USA were investigated by comparing the genetic
diversity and structure of...
Transcriptome analysis of Pseudomonas fluorescensSBW25 showed that 702 genes were differentially regulated in a gacS::Tn5 mutant, with 300 and 402 genes up- and downregulated respectively. Similar to the Gac regulon of other Pseudomonas species, genes involved in motility, biofilm formation, siderophore biosynthesis and oxidative stress were differentially regulated in the...
Background: Functional annotations of large plant genome projects mostly provide information on gene function
and gene families based on the presence of protein domains and gene homology, but not necessarily in
association with gene expression or metabolic and regulatory networks. These additional annotations are necessary
to understand the physiology, development...
Premise of research. A third genus of anatomically preserved conifer seed cones has been recognized from
a Late Jurassic deposit in northeastern Scotland. This cone is described as Bancroftiastrobus digitata Rothwell,
Mapes, Stockey et Hilton.
Methodology. The cone was sectioned with the classic coal ball peel technique and studied and...
Photosynthetic production of organic matter by microscopic oceanic phytoplankton fuels ocean ecosystems
and contributes roughly half of the Earth's net primary production. For 13 years, the Sea-viewing Wide
Field-of-view Sensor (SeaWiFS) mission provided the first consistent, synoptic observations of global ocean
ecosystems. Changes in the surface chlorophyll concentration, the primary...
Ecologists have historically used species-area relationships (SARs) as a tool to understand the spatial distribution of species. Recent work has extended SARs to focus on individual-level distributions to generate individual species area relationships (ISARs). The ISAR approach quantifies whether individuals of a species tend have more or less species richness...
Premise of research. The lianoid habit is found in 125 extant plant families and is most diverse and abundant in structurally complex forests, such as tropical forests. A stem with lianoid anatomy is described from Cretaceous sediments of Hornby Island, British Columbia.
Methodology. The stem segment, 2.5 cm in diameter...
Pythium species are common soilborne oomycetes that occur in forest nursery soils throughout the United States. Numerous species have been described from nursery soils. However, with the exception of P. aphanidermatum, P irregulare, P. sylvaticum, and P ultimum, little is known about the potential for other Pythium species found in...
This scanned article is provided to correct an error on the publisher’s website. The online version has incorrectly given the first author name as “Listen, Aaron” rather than the correct, “Liston, Aaron.” If using this article, please cite the first author correctly.
We investigated habitat attributes related to the occupancy of the globally rare and endangered
epiphytic lichen, Erioderma pedicellatum, in a newly discovered (2009) population center in Denali National
Park and Preserve (DNPP), Alaska. We measured forest, tree and epiphytic lichen community
characteristics on eighty-five systematically selected plots in four study...
We studied the natural hybrid (Fragaria × ananassa subsp. cuneifolia) between two sexually dimorphic octoploid strawberry species (Fragaria virginiana and Fragaria chiloensis) to gain insight into the dynamics of sex chromosomes and the genesis of sexual dimorphism. Male sterility is dominant in both the parental species and thus will be...
Premise of the Study: Hybrid zones provide "natural laboratories" for understanding the processes of selection, reinforcement, and speciation. We sought to gain insight into the degree of introgression and the extent of ecological-phenotypic intermediacy in the natural hybrid strawberry, Fragaria x ananassa subsp. cuneifolia.
Methods: We used whole-plastome sequencing to...
In June 2009, wilted hop bines were observed in a yard in Marion County, OR. The wilt was associated with a stem rot that occurred ∽1 m from the ground near the point where bines are tied together for horticultural purposes. Samples of affected stems were submitted to the Oregon...
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: DNA barcoding of rain forest trees could potentially help biologists identify species and discover new ones. However, DNA barcodes cannot always distinguish between closely related species, and the size and completeness of barcode databases are key parameters for their successful application. We test the ability of rbcL, matK 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...
Pyrenophora tritici-repentis (Ptr), a necrotrophic fungus and the causal agent of tan spot of wheat, produces one or a combination of host-selective toxins (HSTs) necessary for disease development. The two most studied toxins produced by Ptr, Ptr ToxA (ToxA) and Ptr ToxB (ToxB), are proteins that cause necrotic or chlorotic...
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,...
Invasive knotweeds are large perennial herbs in the Polygonaceae in the genus Fallopia that are native to Asia and invasive in North America. They include Fallopia japonica (Japanese knotweed), F. sachalinensis (giant knotweed), and a hybrid species F. x bohemica (Bohemian knotweed). Widespread throughout the continent and difficult to control...
Tannins are a diverse group of plant-produced, polyphenolic compounds with metal-chelating and antimicrobial properties that are prevalent in many soils. Using transcriptomics, we determined that tannic acid, a form of hydrolysable tannin, broadly affects the expression of genes involved in iron and zinc homeostases, sulfur metabolism, biofilm formation, motility, and...
WormBase, dictyBase and The Arabidopsis Information Resource (TAIR) are model organism databases containing information about Caenorhabditis elegans and other nematodes, the social amoeba Dictyostelium discoideum and related Dictyostelids and the flowering plant Arabidopsis thaliana, respectively. Each database curates multiple data types from the primary research literature. In this article, we...
The soil bacterium Pseudomonas protegens Pf-5 (previously called P. fluorescens Pf-5) produces two siderophores, enantio-pyochelin and a compound in the large and diverse pyoverdine family. Using high-resolution mass spectroscopy, we determined the structure of the pyoverdine produced by Pf-5. In addition to producing its own siderophores, Pf-5 also utilizes ferric...
A perithecial ascomycete, Spataporthe taylori gen. et sp. nov., represented by >70 sporocarps is preserved by
cellular permineralization in marine carbonate concretions dated at the Valanginian-Hauterivian boundary (Early
Cretaceous) from Vancouver Island, British Columbia, Canada. The spheroid perithecia with lumina 330–470 µm
wide and 220–320 µm high are densely distributed...
A cylindrical permineralized conifer seed cone has been identified from the Officer Member of the Trowbridge Formation, near Izee, in east-central Oregon. The cone is preserved in a Middle Jurassic (Callovian) marine calcium carbonate concretion, associated with araucarian seed cones, conifer twigs and wood, cycad seeds, fern rachides, and lycopodialean...
A fossil seed cone with characters that have been hypothesized as transitional to the origin of crown group gnetophytes has been discovered in Lower Cretaceous deposits on Vancouver Island, British Columbia, Canada. This cone, described as Protoephedrites eamesii gen. et sp. nov., provides the first anatomically preserved fossil evidence for...
In many databases, biocuration primarily involves literature curation, which usually involves retrieving relevant articles, extracting information that will translate into annotations and identifying new incoming literature. As the volume of biological literature increases, the use of text mining to assist in biocuration becomes increasingly relevant. A number of groups have...
For a variety of infectious diseases, the richness of the community of potential host species has emerged as an important factor in pathogen transmission, whereby a higher richness of host species is associated with a lowered disease risk. The proposed mechanism driving this pattern is an increased likelihood in species-rich...
• Premise of the study: Colonists of even the most inhospitable environments, lichens are present in all terrestrial ecosystems.
Because of their ecological versatility and ubiquity, they have been considered excellent candidates for early colonizers of terrestrial
environments. Despite such predictions, good preservation potential, and the extant diversity of lichenized...