Index Catalog // ScholarsArchive@OSU

Field evaluation of passive capillary samplers for estimating groundwater recharge

Creator:: Louie, Michael J., Shelby, Patrick M., Smesrud, Jason S., Gatchell, Lance O., and Selker, John S.
Abstract:: Passive capillary samplers (PCAPS), which sample water from the vadose zone via a hanging water column in a fiberglass wick, have shown potential to provide superior estimates of soil water flux compared to alternative methods. The objectives of this study were to evaluate the performance of PCAPS under natural rain-fed...
Resource Type:: Article
Full Text:: , • Patrick M. Shelby, 2 Jason S. Smesrud, 3 Lance O. Gatcheil, 4 and John S. Selker s Abstract. Passive

Improved DNase‑seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Creator:: Cumbie, Jason S., Filichkin, Sergei A., and Megraw, Molly
Abstract:: Background: Identifying cis-regulatory elements is critical in understanding the direct and indirect regulatory mechanisms of gene expression. Current approaches include DNase-seq, a technique that combines sensitivity to the nonspecific endonuclease DNase I with high throughput sequencing to identify regions of regulatory DNA on a genome-wide scale. While this method was...
Resource Type:: Article
Full Text:: facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana Jason S

Toward genome-enabled mycology

Creator:: Hibbett, David S., Stajich, Jason E., and Spatafora, Joseph W.
Abstract:: Genome-enabled mycology is a rapidly expanding field that is characterized by the pervasive use of genome-scale data and associated computational tools in all aspects of fungal biology. Genome-enabled mycology is integrative and often requires teams of researchers with diverse skills in organismal mycology, bioinformatics and molecular biology. This issue of...
Resource Type:: Article
Full Text:: mycology David S. Hibbett1 Biology Department, Clark University, Worcester, Massachusetts 01610 Jason E

Estimation of Pyrethrum Flower Number Using Digital Imagery

Creator:: Scott, Jason B., Gent, David H., Hay, Frank S., and Pethybridge, Sarah J.
Abstract:: Flower number is the primary determinant of yield in pyrethrum (Tanacetum cineariifolium). Traditional estimates of flower numbers use physical harvesting of flowers, which is time consuming, destructive, and complicated. The precision of flower number estimates may be highly influenced by spatial heterogeneity of plant density and vigor. Here, we examined...
Resource Type:: Article
Full Text:: Using Digital Imagery Jason B. Scott1,4, David H. Gent2, Frank S. Hay3, and Sarah J. Pethybridge3

Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

Creator:: Burkhardt, Alyssa, Buchanan, Alex, Cumbie, Jason S., Savory, Elizabeth A., Chang, Jeff H., and Day, Brad
Abstract:: Pseudoperonospora cubensis is an obligate pathogen and causative agent of cucurbit downy mildew. To help advance our understanding of the pathogenicity of P. cubensis, we used RNA-Seq to improve the quality of its reference genome sequence. We also characterized the RNA-Seq dataset to inventory transcript isoforms and infer alternative splicing...
Resource Type:: Article
Full Text:: Oomycete Pathogen Pseudoperonospora cubensis Alyssa Burkhardt,1 Alex Buchanan,2 Jason S. Cumbie,2,3

Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus

Creator:: Inglis, Diane O., Skrzypek, Marek S., Liaw, Edward, Moktali, Venkatesh, Sherlock, Gavin, and Stajich, Jason E.
Abstract:: Cryptococcus, a major cause of disseminated infections in immunocompromised patients, kills over 600,000 people per year worldwide. Genes involved in the virulence of the meningitis-causing fungus are being characterized at an increasing rate, and to date, at least 648 Cryptococcus gene names have been published. However, these data are scattered...
Resource Type:: Article

Spatiotemporal Characterization of Sclerotinia Crown Rot Epidemics in Pyrethrum

Creator:: Scott, Jason B., Gent, David H., Pethybridge, Sarah J., and Hay, Frank S.
Abstract:: Sclerotinia crown rot, caused by Sclerotinia minor and S. sclerotiorum, is a disease of pyrethrum in Australia that may cause substantial decline in plant density. The spatiotemporal characteristics of the disease were quantified in 14 fields during three growing seasons. Fitting the binary power law to disease incidence provided slope...
Resource Type:: Article
Full Text:: Crown Rot Epidemics in Pyrethrum Jason B. Scott, Tasmanian Institute of Agriculture (TIA), University

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:: Enrichment Analysis Using Logistic Regression Gu Mi1*, Yanming Di1,2, Sarah Emerson1, Jason S. Cumbie2,3

Individual condition and stream temperature influence early maturation of rainbow and steelhead trout, Oncorhynchus mykiss

Creator:: McMillan, John R., Dunham, Jason B., Reeves, Gordon H., Mills, Justin S., and Jordan, Chris E.
Abstract:: Alternative male phenotypes in salmonine fishes arise from individuals that mature as larger and older anadromous marine-migrants or as smaller and younger freshwater residents. To better understand the processes influencing the expression of these phenotypes we examined the influences of growth in length (fork length) and whole body lipid content...
Resource Type:: Article
Full Text:: maturation of rainbow and steelhead trout, Oncorhynchus mykiss John R. McMillan & Jason B. Dunham & Gordon H

Changes in Distribution and Frequency of Fungi Associated With a Foliar Disease Complex of Pyrethrum in Australia

Creator:: Hay, Frank S., Gent, David H., Pilkington, Stacey J., Pearce, Tamieka L., Scott, Jason B., and Pethybridge, Sarah J.
Abstract:: In Australia, pyrethrum (Tanacetum cinerariifolium) is affected by a foliar disease complex that can substantially reduce green leaf area and yield. Historically, the most important foliar disease of pyrethrum in Australia has been ray blight, caused by Stagonosporopsis tanaceti, and other fungi generally of minor importance. Temporal fluctuations in the...
Resource Type:: Article
Full Text:: Fungi Associated With a Foliar Disease Complex of Pyrethrum in Australia Hay, F. S., Gent, D. H

ScholarsArchive@OSU

Field evaluation of passive capillary samplers for estimating groundwater recharge

Improved DNase‑seq protocol facilitates high resolution mapping of DNase I hypersensitive sites in roots in Arabidopsis thaliana

Toward genome-enabled mycology

Estimation of Pyrethrum Flower Number Using Digital Imagery

Alternative Splicing in the Obligate Biotrophic Oomycete Pathogen Pseudoperonospora cubensis

Literature-Based Gene Curation and Proposed Genetic Nomenclature for Cryptococcus

Spatiotemporal Characterization of Sclerotinia Crown Rot Epidemics in Pyrethrum

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

Individual condition and stream temperature influence early maturation of rainbow and steelhead trout, Oncorhynchus mykiss

Changes in Distribution and Frequency of Fungi Associated With a Foliar Disease Complex of Pyrethrum in Australia

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