Index Catalog // ScholarsArchive@OSU

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Creator:: Fischer, Sylvia E. J., Montgomery, Taiowa A., Zhang, Chi, Fahlgren, Noah, Breen, Peter C., Hwang, Alexia, Sullivan, Christopher M., Carrington, James C., and Ruvkun, Gary
Abstract:: Endogenous small interfering RNAs (siRNAs) are a class of naturally occuring regulatory RNAs found in fungi, plants, and animals. Some endogenous siRNAs are required to silence transposons or function in chromosome segregation; however, the specific roles of most endogenous siRNAs are unclear. The helicase gene eri-6/7 was identified in the...
Resource Type:: Article
Full Text:: pgen.1002369 1..11 The ERI-6/7 Helicase Acts at the First Stage

Inferring phytoplankton carbon and eco-physiological rates from diel cycles of spectral particulate beam-attenuation coefficient

Creator:: Dall'Olmo, G., Boss, E., Behrenfeld, M. J., Westberry, T. K., Courties, C., Prieur, L., Pujo-Pay, M., Hardman-Mountford, N., and Moutin, T.
Abstract:: The diurnal fluctuations in solar irradiance impose a fundamental frequency on ocean biogeochemistry. Observations of the ocean carbon cycle at these frequencies are rare, but could be considerably expanded by measuring and interpreting the inherent optical properties. A method is presented to analyze diel cycles in particulate beam-attenuation coefficient (c[subscript...
Resource Type:: Article
Full Text:: (τ )∑ Ni(τ ) (11) where the sums are over all the size classes. The phytoplank- ton growth rate

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

Creator:: Kasschau, Kristin D., Fahlgren, Noah, Chapman, Elisabeth J., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., and Carrington, James C.
Abstract:: Eukaryotes contain a diversified set of small RNA-guided pathways that control genes, repeated sequences, and viruses at the transcriptional and posttranscriptional levels. Genome-wide profiles and analyses of small RNAs, particularly the large class of 24-nucleotide (nt) short interfering RNAs (siRNAs), were done for wild-type Arabidopsis thaliana and silencing pathway mutants...
Resource Type:: Article
Full Text:: defects over multiple generations [11]. Specific transposons in maize are progressively reactivated in the

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
Full Text:: : Joseph Heitman, Duke University Medical Center, United States of America Received October 11, 2012

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Creator:: Bruskiewich, Richard, Senger, Martin, Davenport, Guy, Ruiz, Manuel, Rouard, Mathieu, Hazekamp, Tom, Takeya, Masaru, Doi, Koji, Satoh, Kouji, Costa, Marcos, Simon, Reinhard, Balaji, Jayashree, Akintunde, Akinnola, Mauleon, Ramil, Wanchana, Samart, Shah, Trushar, Anacleto, Mylah, Portugal, Arllet, Ulat, Victor Jun, Thongjuea, Supat, Braak, Kyle, Ritter, Sebastian, Dereeper, Alexis, Skofic, Milko, Rojas, Edwin, Martins, Natalia, Pappas, Georgios, Alamban, Ryan, Almodiel, Roque, Barboza, Lord Hendrix, Detras, Jeffrey, Manansala, Kevin, Mendoza, Michael Jonathan, Morales, Jeffrey, Peralta, Barry, Valerio, Rowena, Zhang, Yi, Gregorio, Sergio, Hermocilla, Joseph, Echavez, Michael, Yap, Jan Michael, Farmer, Andrew, Schiltz, Gary, Lee, Jennifer, Casstevens, Terry, Jaiswal, Pankaj, Meintjes, Ayton, Wilkinson, Mark, Good, Benjamin, Wagner, James, Morris, Jane, Marshall, David, Collins, Anthony, Kikuchi, Shoshi, Metz, Thomas, McLaren, Graham, and van Hintum, Theo
Abstract:: 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...
Resource Type:: Article
Full Text:: viewers In te rn et Figure 1 [11], SoapLab [12], SSWAP [13], and Tapir [14]. In this pa- per, in the

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Creator:: Mi, Gu, Di, Yanming, Emerson, Sarah, Cumbie, Jason S., and Chang, Jeff H.
Abstract:: When assessing differential gene expression from RNA sequencing data, commonly used statistical tests tend to have greater power to detect differential expression of genes encoding longer transcripts. This phenomenon, called "length bias", will influence subsequent analyses such as Gene Ontology enrichment analysis. In the presence of length bias, Gene Ontology...
Resource Type:: Article
Full Text:: to compute the non-central parameter of the Wallenius distribution [11]. The dependencies between

An Evaluation of Putative Sympatric Speciation within Limnanthes (Limnanthaceae)

Creator:: Meyers, Stephen C., Liston, Aaron, and Meinke, Robert
Abstract:: Limnanthes floccosa ssp. floccosa and L. floccosa ssp. grandiflora are two of five subspecies within Limnanthes floccosa endemic to vernal pools in southern Oregon and northern California. Three seasons of monitoring natural populations have quantified that L. floccosa ssp. grandiflora is always found growing sympatrically with L. floccosa ssp. floccosa...
Resource Type:: Article
Full Text:: , has been criticized for incomplete taxon sampling [11]. The second study [10], which hypothesizes a

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...
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Full Text:: T3SS for host infection [11]. For B. japonicum, we also chose strains based on the genetic diversity

Genetic and Functional Diversification of Small RNA Pathways in Plants

Creator:: Xie, Zhixin, Johansen, Lisa K., Gustafan, Adam M., Kasschau, Kristin D., Lellis, Andrew D., Zilberman, Daniel, Jacobsen, Steven E., and Carrington, James C.
Abstract:: Multicellular eukaryotes produce small RNA molecules (approximately 21–24 nucleotides) of two general types, microRNA (miRNA) and short interfering RNA (siRNA). They collectively function as sequence-specific guides to silence or regulate genes, transposons, and viruses and to modify chromatin and genome structure. Formation or activity of small RNAs requires factors belonging...
Resource Type:: Article
Full Text:: HpaII (Figure 3B, lanes 11–12). Chromatin immunoprecipitation (ChIP) assays were used Figure 3. Effects

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

Creator:: Fahlgren, Noah, Howell, Miya D., Kasschau, Kristin D., Sullivan, Christopher M., Cumbie, Jason S., Givan, Scott A., Law, Theresa F., Grant, Sarah R., Dangl, Jeffrey L., and Carrington, James C.
Abstract:: In plants, microRNAs (miRNAs) comprise one of two classes of small RNAs that function primarily as negative regulators at the posttranscriptional level. Several MIRNA genes in the plant kingdom are ancient, with conservation extending between angiosperms and the mosses, whereas many others are more recently evolved. Here, we use deep...
Resource Type:: Article
Full Text:: small RNAs is potentially large in animals and plants [11– 13]. In humans, for example, computational

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

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...
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Full Text:: 1 LO C _O S 03 G 05 71 0 R 3 LO C _O S 07 G 25 59 0 R 1 LO C _O S 10 G 26 11 0 R 1

Response of the nitrogen-fixing lichen Lobaria pulmonaria to phosphorus, molybdenum, and vanadium

Creator:: Marks, Jade A., Pett-Ridge, Julie C., Perakis, Steven S., Allen, Jessica L., and McCune, Bruce
Abstract:: 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...
Resource Type:: Article
Full Text:: only and do not include 2012 data for which growth rates are not available. v www.esajournals.org 11

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
Full Text:: in the absolute analysis and 11 did not have a corresponding Affymetrix probe ID (Additional file 3

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

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...
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Full Text:: USA 104: 19029–19033. 11. Webb CO, Ackerly DD, McPeek MA, Donoghue MJ (2002) Phylogenies and

ScholarsArchive@OSU

The ERI-6/7 Helicase Acts at the First Stage of an siRNA Amplification Pathway That Targets Recent Gene Duplications

Inferring phytoplankton carbon and eco-physiological rates from diel cycles of spectral particulate beam-attenuation coefficient

Genome-Wide Profiling and Analysis of Arabidopsis siRNAs

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

The Generation Challenge Programme Platform: Semantic Standards and Workbench for Crop Science

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

An Evaluation of Putative Sympatric Speciation within Limnanthes (Limnanthaceae)

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

Genetic and Functional Diversification of Small RNA Pathways in Plants

High-Throughput Sequencing of Arabidopsis microRNAs : Evidence for Frequent Birth and Death of MIRNA Genes

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

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

Response of the nitrogen-fixing lichen Lobaria pulmonaria to phosphorus, molybdenum, and vanadium

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

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

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

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