Index Catalog // ScholarsArchive@OSU

An experimental reintroduction of Pleuropogon oregonus, a rare wetland grass native to Oregon

Creator:: Groberg, Matthew G.
Abstract:: Pleuropogon oregonus Chase is a rare wetland grass endemic to eastern Oregon. The species is composed of two widely separated populations, one in Lake County and one in Union County. In order to reduce the risk of extinction, the Oregon Department of Agriculture Native Plant Conservation Program initiated several reintroduction...
Resource Type:: Masters Thesis

Sweet corn diseases and their management in the PNW : Seed treatment evaluations and development of Fusarium-free seed : Report to the Agricultural Research Foundation for the Oregon Processed Vegetable Commission, December 2013

Creator:: Ocamb, Cynthia M.
Abstract:: Sweet corn is susceptible to various pathogenic Fusarium species and has been long known to be subject to early season diseases of seed rot and seedling blight as well as root rot and later season problems with stalk rot and ear rots. More recently, fields in the Willamette Valley of...
Resource Type:: Technical Report

Detection of Plasmodiophora brassicae (causal agent of Clubroot) in vegetable production fields of the Pacific Northwest : Report to the Agricultural Research Foundation for the Oregon Processed Vegetable Commission, December 2013

Creator:: Ocamb, Cynthia M.
Abstract:: Clubroot, caused by Plasmodiophora brassicae, affects all species of the Crucifer family, including wild mustard. It is a fungus-like microorganism that can persist in soil in the form of durable resting spores for 18 years or longer after an infected crop. These resting spores can be spread through any means...
Resource Type:: Technical Report

Phytophthora Have Distinct Endogenous Small RNA Populations That Include Short Interfering and microRNAs

Creator:: Fahlgren, Noah, Bollmann, Stephanie R., Kasschau, Kristin D., Cuperus, Josh T., Press, Caroline M., Sullivan, Christopher M., Chapman, Elisabeth J., Hoyer, J. Steen, Gilbert, Kerrigan B., Grunwald, Niklaus J., and Carrington, James C.
Abstract:: 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...
Resource Type:: Article

Lichen communities and caribou habitat in Denali National Park and Preserve, Alaska, USA

Creator:: Nelson, Peter R.
Abstract:: Lichens play many important roles in subarctic terrestrial ecosystems by fixing nitrogen, colonizing rock and gravel, stabilizing otherwise bare soil, adding significantly to vegetation biodiversity and serving as the primary food for caribou in the winter. In these chapters, I analyzed lichen community and ecological trait structure along environmental gradients,...
Resource Type:: Dissertation

A virocentric perspective on the evolution of life

Creator:: Koonin, Eugene V. and Dolja, Valerian V.
Abstract:: 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...
Resource Type:: Article

Identification of Phytophthora infestans US-8 lineage through genetic markers

Creator:: Fritz, Eric and Knaus, Brian
Resource Type:: Presentation

Presence and pathogenicity of Fusarium and Verticillium species in commercial red radish (Raphanus sativus) seed production in the Willamette Valley of Oregon

Creator:: Bomberger, Rachel A.
Abstract:: Commercial radish seed producers in the Willamette Valley of Oregon have observed a late season wilt in their seed fields. Twenty-two fields were surveyed for wilt in the Willamette Valley during June through August 2012 and 2013. Plants exhibiting wilt symptoms were collected from the fields and examined for vascular...
Resource Type:: Masters Thesis

Characterisation of virulence reactions for Heterodera avenae populations from two localities in Algeria

Creator:: Haddadi, Fatima, Mokabli, Aissa, and Smiley, Richard W.
Abstract:: 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...
Resource Type:: Article

Space-based lidar measurements of global ocean carbon stocks

Creator:: Behrenfeld, Michael J., Hu, Yongxiang, Hostetler, Chris A., Dall’Olmo, Giorgio, Rodier, Sharon D., Hair, John W., and Trepte, Charles R.
Abstract:: 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...
Resource Type:: Article

Histological comparisons of needle tissues of four species of white pine infected by Cronartium ribicola

Creator:: Sweeney, Katarina
Abstract:: Hypersensitive response-like (HR-like) needle reactions to infection by the white pine blister rust pathogen, Cronartium ribicola, have been reported for several species of five needle pines native to western North America. The best-studied examples are in Pinus monticola and P. lambertiana. In these species a "needle spot" phenotype has been...
Resource Type:: Masters Thesis

Regional to global assessments of phytoplankton dynamics from the SeaWiFS mission

Creator:: Siegel, D. A., Behrenfeld, Michael J., Maritorena, S., McClain, C. R., Antoine, D., Bailey, S. W., Bontempi, P. S., Boss, E. S., Dierssen, H. M., Doney, S. C., Eplee, R. E. Jr., Evans, R. H., Feldman, G. C., Fields, E., Franz, B. A., Kuring, N. A., Mengelt, C., Nelson, N. B., Patt, F. S., Robinson, W. D., Sarmiento, J. L., Swan, C. M., Werdell, P. J., Westberry, T. K., Wilding, J. G., and Yoder, J. A.
Abstract:: 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...
Resource Type:: Article

The Gac regulon of Pseudomonas fluorescens SBW25

Creator:: Cheng, Xu, de Bruijn, Irene, van der Voort, Menno, Loper, Joyce E., and Raaijmakers, Jos M.
Abstract:: 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...
Resource Type:: Article

Identification of Myosin XI Receptors in Arabidopsis Defines a Distinct Class of Transport Vesicles

Creator:: Peremyslov, Valera V., Morgun, Eva A., Kurth, Elizabeth G., Makarova, Kira S., Koonin, Eugene V., and Dolja, Valerian V.
Abstract:: 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...
Resource Type:: Article

Influence of Raman scattering on ocean color inversion models

Creator:: Westberry, Toby K., Boss, Emmanuel, and Lee, Zhongping
Abstract:: 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...
Resource Type:: Article

The phylogenetic placement of hypocrealean insect pathogens in the genus Polycephalomyces: An application of One Fungus One Name

Creator:: Kepler, Ryan, Ban, Sayaka, Nakagiri, Akira, Bischoff, Joseph, Hywel-Jones, Nigel, Owensby, Catherine Alisha, and Spatafora, Joseph W.
Abstract:: 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...
Resource Type:: Article

Within-population genetic structure differs between two sympatric sister-species of ectomycorrhizal fungi, Rhizopogon vinicolor and R. vesiculosus

Creator:: Dunham, Susie M., Mujic, Alija Bajro, Spatafora, Joseph W., and Kretzer, Annette M.
Abstract:: 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...
Resource Type:: Article

Detecting continuous lichen abundance for mapping winter caribou forage at landscape spatial scales

Creator:: Nelson, Peter R., Roland, Carl, Macander, Matthew J., and McCune, Bruce
Abstract:: 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...
Resource Type:: Article

pA506, a Conjugative Plasmid of the Plant Epiphyte Pseudomonas fluorescens A506

Creator:: Stockwell, Virginia O., Davis, Edward W., II, Carey, Alyssa, Shaffer, Brenda T., Mavrodi, Dmitri V., Hassan, Karl A., Hockett, Kevin, Thomashow, Linda S., Paulsen, Ian T., and Lopera, Joyce E.
Abstract:: 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...
Resource Type:: Article

Annual cycles of ecological disturbance and recovery underlying the subarctic Atlantic spring plankton bloom

Creator:: Behrenfeld, Michael J., Doney, Scott C., Lima, Ivan, Boss, Emmanuel S., and Siegel, David A.
Abstract:: 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...
Resource Type:: Article

The Genome of Tolypocladium inflatum: Evolution, Organization, and Expression of the Cyclosporin Biosynthetic Gene Cluster

Creator:: Bushley, Kathryn E., Raja, Rajani, Jaiswal, Pankaj, Cumbie, Jason S., Nonogaki, Mariko, Boyd, Alexander E., Owensby, C. Alisha, Knaus, Brian J., Elser, Justin, Miller, Daniel, Di, Yanming, McPhail, Kerry L., and Spatafora, Joseph W.
Abstract:: 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...
Resource Type:: Article

Pathogenicity of Phytophthora species from Oregon waterways

Creator:: Navarro, Sarah M.
Abstract:: Described as one of the most destructive pathogens of agricultural crops and forest trees, Phytophthora is a genus of microorganisms containing over 100 known species. Phytophthora alni has caused collar and root disease in alders throughout Europe and a form of the species has recently been isolated in North America....
Resource Type:: Masters Thesis

Diversity of ancient conifers: The jurassic seed cone bancroftiastrobus digitata gen. et sp. nov. (coniferales)

Creator:: Rothwell, Gar W., Mapes, Gene, Stockey, Ruth A., and Hilton, Jason
Abstract:: 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...
Resource Type:: Article

A ranunculalean liana stem from the cretaceous of British Columbia, Canada: Atli morinii gen. et sp nov.

Creator:: Smith, Selena Y., Little, Stefan A., Cooper, Ranessa L., Burnham, Robyn J., and Stockey, Ruth A.
Abstract:: 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...
Resource Type:: Article

Pathogenicity and Virulence of Pythium Species Obtained from Forest Nursery Soils on Douglas-Fir Seedlings

Creator:: Weiland, Jerry E., Beck, Bryan R., and Davis, Anne
Abstract:: 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...
Resource Type:: Article

The Use and Role of Predictive Systems in Disease Management

Creator:: Gent, David H., Mahaffee, Walter F., McRoberts, Neil, and Pfender, William F.
Abstract:: 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...
Resource Type:: Article

A Phylogenetic Perspective on the Individual Species- Area Relationship in Temperate and Tropical Tree Communities

Creator:: Yang, Jie, Swenson, Nathan G., Cao, Min, Chuyong, George B., Ewango, Corneille E. N., Howe, Robert, Kenfack, David, Thomas, Duncan, Wolf, Amy, and Lin, Luxiang
Abstract:: 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...
Resource Type:: Article

Wind farm potential is higher in prime habitat for uncommon soil crust lichens

Creator:: Root, Heather T., McCune, Myrica, and McCune, Bruce
Abstract:: 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...
Resource Type:: Article

Sex-determining chromosomes and sexual dimorphism: insights from genetic mapping of sex expression in a natural hybrid Fragaria ×ananassa subsp. cuneifolia

Creator:: Govindarajulu, Rajanikanth, Liston, Aaron, and Ashman, Tia-Lynn
Abstract:: 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...
Resource Type:: Article

Bioclimatic, ecological, and phenotypic intermediacy and high genetic admixture in a natural hybrid of octoploid strawberries

Creator:: Salamone, Isabella, Govindarajulu, Rajanikanth, Falk, Stacey, Parks, Matthew, Liston, Aaron, and Ashnam, Tia-Lynn
Abstract:: 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...
Resource Type:: Article

Ca. Nitrososphaera and Bradyrhizobium are inversely correlated and related to agricultural practices in long-term field experiments

Creator:: Zhalnina, Kateryna, de Quadros, Patricia D., Gano, Kelsey A., Davis-Richardson, Austin, Fagen, Jennie R., Brown, Christopher T., Giongo, Adriana, Drew, Jennifer C., Sayavedra-Soto, Luis A., Arp, Daniel J., Camargo, Flavio A. O., Daroub, Samira H., Clark, Ian M., McGrath, Steve P., Hirsch, Penny R., and Triplett, Eric W.
Abstract:: 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...
Resource Type:: Article

Patterns in the occupancy and abundance of the globally rare lichen Erioderma pedicellatum in Denali National Park and Preserve, Alaska

Creator:: Stehn, Sarah E., Nelson, Peter R., Roland, Carl A., and Jones, Jennifer R.
Abstract:: 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...
Resource Type:: Article

Grapevine leafroll-associated virus 3

Creator:: Maree, Hans J., Almeida, Rodrigo P. P., Bester, Rachelle, Chooi, Kar Mun, Cohen, Daniel, Dolja, Valerian V., Fuchs, Marc F., Golino, Deborah A., Jooste, Anna E. C., Martelli, Giovanni P., Naidu, Rayapati A., Rowhani, Adib, Saldarelli, Pasquale, and Burger, Johan T.
Abstract:: 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...
Resource Type:: Article

The closterovirus-derived gene expression and RNA interference vectors as tools for research and plant biotechnology

Creator:: Dolja, Valerian V. and Koonin, Eugene V.
Abstract:: 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...
Resource Type:: Article

The Plant Actin Cytoskeleton Responds to Signals from Microbe-Associated Molecular Patterns

Creator:: Henty-Ridilla, Jessica L., Shimono, Masaki, Li, Jiejie, Chang, Jeff H., Day, Brad, and Staiger, Christopher J.
Abstract:: 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...
Resource Type:: Article

How Effective Are DNA Barcodes in the Identification of African Rainforest Trees?

Creator:: Parmentier, Ingrid, Duminil, Jérôme, Kuzmina, Maria, Philippe, Morgane, Thomas, Duncan W., Kenfack, David, Chuyong, George B., Cruaud, Corinne, and Hardy, Olivier J.
Abstract:: 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...
Resource Type:: Article

Morphological and genetic characterisation of Beauveria sinensis sp. nov. from China

Creator:: Chen, Ming-Jun, Huang, Bo, Li, Zeng-Zhi, and Spatafora, Joseph W.
Abstract:: 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...
Resource Type:: Article

Fungal endophyte diversity in foliage of native and cultivated Rhododendron species determined by culturing, ITS sequencing, and pyrosequencing

Creator:: Raizen, Nathaniel L.
Abstract:: Western Oregon is home to native Rhododendron species and is the center for cultivated Rhododendron production in the United States. These Rhododendron spp. are known to be infected with fungal endophytes. However, the community structure of these endophytes in native and cultivated Rhododendron is poorly understood. Our study targeted the...
Resource Type:: Masters Thesis

Sequencing and De Novo Transcriptome Assembly of Brachypodium sylvaticum (Poaceae)

Creator:: Fox, Samuel E., Preece, Justin, Kimbrel, Jeffrey A., Marchini, Gina L., Sage, Abigail, Youens-Clark, Ken, Cruzan, Mitchell B., and Jaiswal, Pankaj
Abstract:: 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...
Resource Type:: Article

A Perithecial Sordariomycete (Ascomycota, Diaporthales) from the Lower Cretaceous of Vancouver Island, British Columbia, Canada

Creator:: Bronson, Allison W., Klymiuk, Ashley A., Stockey, Ruth A., and Tomescu, Alexandru M. F.
Abstract:: 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...
Resource Type:: Article

Maize Metabolic Network Construction and Transcriptome Analysis

Creator:: Monaco, Marcela K., Sen, Taner Z., Dharmawardhana, Palitha D., Ren, Liya, Schaeffer, Mary, Naithani, Sushma, Amarasinghe, Vindhya, Thomason, Jim, Harper, Lisa, Gardiner, Jack, Cannon, Ethalinda K.S., Lawrence, Carolyn J., Ware, Doreen, and Jaiswal, Pankaj
Abstract:: 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...
Resource Type:: Article

Evolution and Phylogeny of Gnetophytes: Evidence From the Anatomically Preserved Seed Cone Protoephedrites Eamesii gen. et sp nov. and the Seeds of Several Bennettitalean Species

Creator:: Rothwell, Gar W. and Stockey, Ruth A.
Abstract:: 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...
Resource Type:: Article

Pararaucaria carrii sp nov., anatomically preserved evidence for the conifer family cheirolepidiaceae in the northern hemisphere

Creator:: Stockey, Ruth A. and Rothwell, Gar W.
Abstract:: 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...
Resource Type:: Article

The effect of zinc limitation on the transcriptome of Pseudomonas protegens Pf-5

Creator:: Lim, Chee Kent, Hassan, Karl A., Penesyan, Anahit, Loper, Joyce E., and Paulsen, Ian T.
Abstract:: Zinc is an important nutrient but can be lacking in some soil environments, influencing the physiology of soil-dwelling bacteria. Hence, we studied the global effect of zinc limitation on the transcriptome of the rhizosphere biocontrol strain Pseudomonas protegens Pf-5 (formerly Pseudomonas fluorescens). We observed that the expression of the putative...
Resource Type:: Article

Risk of Exposure to Eastern Equine Encephalomyelitis Virus Increases with the Density of Northern Cardinals

Creator:: Estep, Laura K., McClure, Christopher J. W., Vander Kelen, Patrick, Burkett-Cadena, Nathan D., Sickerman, Stephen, Hernandez, José, Jinright, Joseph, Hunt, Brenda, Lusk, John, Hoover, Victor, Armstrong, Keith, Stark, Lillian M., Hill, Geoffrey E., and Unnasch, Thomas R.
Abstract:: 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...
Resource Type:: Article

Mutualistic Co-evolution of Type III Effector Genes in Sinorhizobium fredii and Bradyrhizobium japonicum

Creator:: Kimbrel, Jeffrey A., Thomas, William J., Jiang, Yuan, Creason, Allison L., Thireault, Caitlin A., Sachs, Joel L., and Chang, Jeff H.
Abstract:: 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...
Resource Type:: Article

Effect of Tannic Acid on the Transcriptome of the Soil Bacterium Pseudomonas protegens Pf-5

Creator:: Lim, Chee Kent, Penesyan, Anahit, Hassan, Karl A., Loper, Joyce E., and Paulsen, Ian T.
Abstract:: 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...
Resource Type:: Article

Infection of Brachypodium distachyon by Formae Speciales of Puccinia graminis: Early Infection Events and Host-Pathogen Incompatibility

Creator:: Figueroa, Melania, Alderman, Stephen, Garvin, David F., and Pfender, William F.
Abstract:: Puccinia graminis causes stem rust, a serious disease of cereals and forage grasses. Important formae speciales of P. graminis and their typical hosts are P. graminis f. sp. tritici (Pg-tr) in wheat and barley, P. graminis f. sp. lolii (Pg-lo) in perennial ryegrass and tall fescue, and P. graminis f....
Resource Type:: Article

Invaded range of the blackberry pathogen Phragmidium violaceum in the Pacific Northwest of the USA and the search for its provenance

Creator:: Morin, Louise, Gomez, Don R., Evans, Katherine J., Neill, Tara M., Mahaffee, Walt F., and Linde, Celeste C.
Abstract:: 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...
Resource Type:: Article

Honeggeriella complexa gen. et sp. nov., a heteromerous lichen from the lower cretaceous of Vancouver Island (British Columbia, Canada)

Creator:: Matsunaga, Kelly K. S., Stockey, Ruth A., and Tomescu, Alexandru M. F.
Abstract:: • 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...
Resource Type:: Article

Ferric-Pyoverdine Recognition by Fpv Outer Membrane Proteins of Pseudomonas protegens Pf-5

Creator:: Hartney, Sierra L., Mazurier, Sylvie, Girard, Maeva K., Mehnaz, Samina, Davis, Edward W. II, Gross, Harald, Lemanceau, Philippe, and Loper, Joyce E.
Abstract:: 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...
Resource Type:: Article

The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

Creator:: Cooper, Laurel, Walls, Ramona L., Elser, Justin, Gandolfo, Maria A., Stevenson, Dennis W., Smith, Barry, Preece, Justin, Athreya, Balaji, Mungall, Christopher J., Rensing, Stefan, Hiss, Manuel, Lang, Daniel, Reski, Ralf, Berardini, Tanya Z., Li, Donghui, Huala, Eva, Schaeffer, Mary, Menda, Naama, Arnaud, Elizabeth, Shrestha, Rosemary, Yamazaki, Yukiko, and Jaiswal, Pankaj
Abstract:: 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...
Resource Type:: Article

Comparative Genome Structure, Secondary Metabolite, and Effector Coding Capacity across Cochliobolus Pathogens

Creator:: Condon, Bradford J., Leng, Yueqiang, Wu, Dongliang, Bushley, Kathryn E., Ohm, Robin A., Otillar, Robert, Martin, Joel, Schackwitz, Wendy, Grimwood, Jane, MohdZainudin, NurAinIzzati, Xue, Chunsheng, Wang, Rui, Manning, Viola A., Dhillon, Braham, Tu, Zheng Jin, Steffenson, Brian J., Salamov, Asaf, Sun, Hui, Lowry, Steve, LaButti, Kurt, Han, James, Copeland, Alex, Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Baker, Scott E., Ciuffetti, Lynda M., Grigoriev, Igor V., Zhong, Shaobin, and Turgeon, B. Gillian
Abstract:: 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...
Resource Type:: Article

An overview of the BioCreative 2012 Workshop Track III: interactive text mining task

Creator:: Arighi, Cecilia N., Carterette, Ben, Cohen, K. Bretonnel, Krallinger, Martin, Wilbur, W. John, Fey, Petra, Dodson, Robert, Cooper, Laurel, Van Slyke, Ceri E., Dahdul, Wasila, Mabee, Paula, Li, Donghui, Harris, Bethany, Gillespie, Marc, Jimenez, Silvia, Roberts, Phoebe, Matthews, Lisa, Becker, Kevin, Drabkin, Harold, Bello, Susan, Licata, Luana, Chatr-aryamontri, Andrew, Schaeffer, Mary L., Park, Julie, Haendel, Melissa, Van Auken, Kimberly, Li, Yuling, Chan, Juancarlos, Muller, Hans-Michael, Cui, Hong, Balhoff, James P., Wu, Johnny Chi-Yang, Lu, Zhiyong, Wei, Chih-Hsuan, Tudor, Catalina O., Raja, Kalpana, Subramani, Suresh, Natarajan, Jeyakumar, Cejuela, Juan Miguel, Dubey, Pratibha, and Wu, Cathy
Abstract:: 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...
Resource Type:: Article

Efficacy and host specificity compared between two populations of the psyllid Aphalara itadori, candidates for biological control of invasive knotweeds in North America

Creator:: Grevstad, Fritzi, Shaw, Richard, Bourchier, Robert, Sanguankeo, Paolo, Cortat, Ghislaine, and Reardon, Richard C.
Abstract:: 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...
Resource Type:: Article

WikiPathways for plants: a community pathway curation portal and a case study in rice and arabidopsis seed development networks

Creator:: Hanumappa, Mamatha, Preece, Justin, Elser, Justin, Nemeth, Denise, Bono, Gina, Wu, Kenny, and Jaiswal, Pankaj
Abstract:: 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...
Resource Type:: Article

Some marine algae on tsunami debris

Creator:: Hansen, Gayle I.
Abstract:: The Great Tohoku Earthquake and Tsunami of March 2011 generated nearly 1.5 million tons of floating debris. After 1-5 years of drifting with the currents across the Pacific, many debris items reached the NE Pacific coast carrying Japanese marine species that could colonize our shores. More than 84 marine algal...
Resource Type:: Poster

Comparative Genomics of a Plant-Pathogenic Fungus, Pyrenophora tritici-repentis, Reveals Transduplication and the Impact of Repeat Elements on Pathogenicity and Population Divergence

Creator:: Manning, Viola A., Pandelova, Iovanna, Dhillon, Braham, Wilhelm, Larry J., Goodwin, Stephen B., Berlin, Aaron M., Figueroa, Melania, Freitag, Michael, Hane, James K., Henrissat, Bernard, Holman, Wade H., Kodira, Chinnappa D., Martin, Joel, Oliver, Richard P., Robbertse, Barbara, Schackwitz, Wendy, Schwartz, David C., Spatafora, Joseph W., Turgeon, B. Gillian, Yandava, Chandri, Young, Sarah, Zhou, Shiguo, Zeng, Qiandong, Grigoriev, Igor V., Ma, Li-Jun, and Ciuffetti, Lynda M.
Abstract:: Pyrenophora tritici-repentis is a necrotrophic fungus causal to the disease tan spot of wheat, whose contribution to crop loss has increased significantly during the last few decades. Pathogenicity by this fungus is attributed to the production of host-selective toxins ( HST), which are recognized by their host in a genotype-specific...
Resource Type:: Article

A genome scale metabolic network for rice and accompanying analysis of tryptophan, auxin and serotonin biosynthesis regulation under biotic stress

Creator:: Dharmawardhana, Palitha, Ren, Liya, Amarasinghe, Vindhya, Monaco, Marcela, Thomason, Jim, Ravenscroft, Dean, McCouch, Susan, Ware, Doreen, and Jaiswal, Pankaj
Abstract:: 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...
Resource Type:: Article

Insights into phylogeny, sex function and age of Fragaria based on whole chloroplast genome sequencing

Creator:: Njuguna, Wambui, Liston, Aaron, Cronn, Richard, Ashman, Tia-Lynn, and Bassil, Nahla
Abstract:: The cultivated strawberry is one of the youngest domesticated plants, developed in France in the 1700s from chance hybridization between two western hemisphere octoploid species. However, little is known about the evolution of the species that gave rise to this important fruit crop. Phylogenetic analysis of chloroplast genome sequences of...
Resource Type:: Article

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