Index Catalog // ScholarsArchive@OSU

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
Full Text:: identification (71–88%). Using a single marker, best results for species identification were obtained with trnH

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
Full Text:: of California Press, Berkeley, CA, USA. 30. Tringe SG, Rubin EM. 2005. Metagenomics: DNA

Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus)

Creator:: Schroeder, Hilke, Cronn, Richard, Yanbaev, Yulai, Jennings, Tara, Mader, Malte, Degen, Bernd, and Kersten, Birgit
Abstract:: 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...
Resource Type:: Article
Full Text:: 135 123 86/71 (30) Q. dentata 9 (5) 174 179 135 123 86/71 (30) 1 The number of individuals tested

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
Full Text:: 48:7420 –7431. 36. Lim CK, Hassan KA, Tetu SG, Loper JE, Paulsen IT. 2012. The effect of iron

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
Full Text:: 73,190 SNPs/bp 5008 508 Multiallellic SNP 1250 6648 Small indels found 71% 71% Small indels 1843 4282

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
Full Text:: symbiosis. Mol Microbiol 71:92–106; 12Rodrigues J et al. (2007) NopM and NopD are rhizobial nodulation

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
Full Text:: ct o m e , a n d SG D b g e n e -c e n tr ic : 1 0 fi rs t- ra n k e d a b st ra ct s fo r 4 p ro

Orbilia ultrastructure, character evolution and phylogeny of Pezizomycotina

Creator:: Kumar, T.K. Arun, Healy, Rosanne, Spatafora, Joseph W., Blackwell, Meredith, and McLaughlin, David J.
Abstract:: Molecular phylogenctic analyses indicate that the monophyletic classes Orbiliomycetes and Pezizomycetes are among the earliest diverging branches of Pezizomycotina, the largest subphylum of the Ascomycota. Although Orbiliomycetes is resolved as the most basal lineage in some analyses, molecular support for the node resolving the relationships between the two classes is...
Resource Type:: Article
Full Text:: Euascomycetes. In: Gull K, Oliver SG, eds. The fungal nucleus. Cambridge: Cambridge Univ. Press. p 37–61

Formation of Complexes at Plasmodesmata for Potyvirus Intercellular Movement Is Mediated by the Viral Protein P3N-PIPO

Creator:: Wei, Taiyun, Zhang, Changwei, Hong, Jian, Xiong, Ruyi, Kasschau, Krisitin D., Zhou, Xueping, Carrington, James C., and Wang, Aiming
Abstract:: Intercellular transport of viruses through cytoplasmic connections, termed plasmodesmata (PD), is essential for systemic infection in plants by viruses. Previous genetic and ultrastructural data revealed that the potyvirus cyclindrical inclusion (CI) protein is directly involved in cell-to-cell movement, likely through the formation of conical structures anchored to and extended through...
Resource Type:: Article
Full Text:: , Findlay K, Shaw JG, Lomonossoff GP, Qiu SG, Linstead P, et al. (1997) The coat and cylindrical inclusion

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
Full Text:: 71 65 72 71 100 75 100 97 99 100 99 86 59 60 91 100 100 59 100 97 82 87 100 52

ScholarsArchive@OSU

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

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

Development of Molecular Markers for Determining Continental Origin of Wood from White Oaks (Quercus L. sect. Quercus)

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

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

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

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

Orbilia ultrastructure, character evolution and phylogeny of Pezizomycotina

Formation of Complexes at Plasmodesmata for Potyvirus Intercellular Movement Is Mediated by the Viral Protein P3N-PIPO

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

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