Index Catalog // ScholarsArchive@OSU

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
Full Text:: regulation under biotic stress Palitha Dharmawardhana1, Liya Ren2, Vindhya Amarasinghe1, Marcela Monaco2, Jim

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
Full Text:: , Vindhya Amarasinghe, Jim Thomason, Lisa Harper, Jack Gardiner, Ethalinda K.S. Cannon, Carolyn J. Lawrence

Gramene database in 2010: updates and extensions

Creator:: Youens-Clark, Ken, Buckler, Ed, Casstevens, Terry, Chen, Charles, DeClerck, Genevieve, Derwent, Paul, Dharmawardhana, Palitha, Jaiswal, Pankaj, Kersey, Paul, Karthikeyan, A. S., Lu, Jerry, McCouch, Susan R., Ren, Liya, Spooner, William, Stein, Joshua C., Thomason, Jim, Wei, Sharon, and Ware, Doreen
Abstract:: 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...
Resource Type:: Article
Full Text:: Lu1, Susan R. McCouch4, Liya Ren1, William Spooner1, Joshua C. Stein1, Jim Thomason1, Sharon Wei1 and

A dynamic leaf gas-exchange strategy is conserved in woody plants under changing ambient CO₂: evidence from carbon isotope discrimination in paleo and CO₂ enrichment studies

Creator:: Voelker, Steven L., Brooks, J. Renée, Meinzer, Frederick C., Anderson, Rebecca, Bader, Martin K.-F., Battipaglia, Giovanna, Becklin, Katie M., Beerling, David, Bert, Didier, Betancourt, Julio L., Dawson, Todd E., Domec, Jean-Christophe, Guyette, Richard P., Körner, Christian, Leavitt, Steven W., Linder, Sune, Marshall, John D., Mildner, Manuel, Ogée, Jérôme, Panyushkina, Irina, Plumpton, Heather J., Pregitzer, Kurt S., Saurer, Matthias, Smith, Andrew R., Siegwolf, Rolf T. W., Stambaugh, Michael C., Talhelm, Alan F., Tardif, Jacques C., Van de Water, Peter K., Ward, Joy K., and Wingate, Lisa
Abstract:: Rising atmospheric [CO₂], cₐ, is expected to affect stomatal regulation of leaf gas-exchange of woody plants, thus influencing energy fluxes as well as carbon (C), water, and nutrient cycling of forests. Researchers have proposed various strategies for stomatal regulation of leaf gas-exchange that include maintaining a constant leaf internal [CO₂],...
Resource Type:: Article
Full Text:: thank Dr. Jeff Warren, Dr. Jon Keeley, Dr. Jim Ehleringer and an anonymous reviewer for providing

Identification and characterization of type III effector proteins in plant-associated bacteria

Creator:: Thomas, William J.
Abstract:: Symbioses between microbes and multicellular eukaryotes are found in all biomes, and encompass a spectrum of symbiotic lifestyles that includes parasitism and disease, commensalism, and mutually beneficial interdependent host-microbe relationships. Regardless of outcome, these symbiotic lifestyles are governed by a complex molecular "courtship" between microbe and potential host. This courtship...
Resource Type:: Dissertation

Nitrogen management and variety selection for dryland production of hard red winter wheat in northeastern Oregon

Creator:: Jepsen, Daniel R.
Abstract:: Proper nitrogen (N) management and variety selection are important for profitable hard red winter (HRW) wheat production in the dryland growing regions of northeastern Oregon. In these dryland systems, N management for grain yield and grain protein concentration (GPC) is challenging due to climatic and year-to-year variation in production environments....
Resource Type:: Masters Thesis
Full Text:: time I come to him for academic or field expertise. Thanks also go to Drs. Jim Peterson, Steve

Cellular Recognition, Division, and Proliferation in the Cnidarian-Dinoflagellate Symbiosis

Creator:: Tivey, Trevor R.
Abstract:: Cnidarians and their symbiotic dinoflagellates form a productive mutualism that shapes marine environments. In this symbiosis, dinoflagellate species from the family Symbiodiniacea reside within cnidarian host gastrodermal cells and provide the host with photosynthetically fixed carbon in exchange for host metabolites. This nutritional exchange allows both partners to thrive in...
Resource Type:: Dissertation
Full Text:: members of my committee, Barb Taylor, Tom Sharpton, Eli Meyer, Mark Leid, and Jim Strother for their

Genome-enabled discovery and characterization of type III effector-encoding genes of plant symbiotic bacteria

Creator:: Kimbrel, Jeffrey A.
Abstract:: Symbiosis is the close and protracted interaction between organisms. The molecular interactions that occur during symbiosis are complex with multiple barriers that must be overcome. Many Gram-negative, host-associated bacteria use a type III secretion system to mediate associations with their eukaryotic hosts. This secretion system is a specialized apparatus for...
Resource Type:: Dissertation

Wildlife Health in Managed Forests : Immunity and Infectious Diseases in Wild Rodents of Oregon

Creator:: Hanselmann, Rhea
Abstract:: With continual and worldwide human population growth, our impact on the natural environment expands and intensifies every day. We consume natural resources, burn fossil fuels, and release toxic compounds into the air, water, and earth. We build roads that fragment the landscape, construct new settlements, and develop agricultural lands in...
Resource Type:: Dissertation
Full Text:: University of Health Sciences; Matt Betts, Tom Manning, and Jim Rivers at OSU’s Department of Forest

ScholarsArchive@OSU

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

Maize Metabolic Network Construction and Transcriptome Analysis

Gramene database in 2010: updates and extensions

A dynamic leaf gas-exchange strategy is conserved in woody plants under changing ambient CO₂: evidence from carbon isotope discrimination in paleo and CO₂ enrichment studies

Identification and characterization of type III effector proteins in plant-associated bacteria

Nitrogen management and variety selection for dryland production of hard red winter wheat in northeastern Oregon

Cellular Recognition, Division, and Proliferation in the Cnidarian-Dinoflagellate Symbiosis

Genome-enabled discovery and characterization of type III effector-encoding genes of plant symbiotic bacteria

Wildlife Health in Managed Forests : Immunity and Infectious Diseases in Wild Rodents of Oregon

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