Index Catalog // ScholarsArchive@OSU

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

Creator:: Muñoz‐Amatriaín, Maria, Lonardi, Stefano, Luo, MingCheng, Madishetty, Kavitha, Svensson, Jan T., Moscou, Matthew J., Wanamaker, Steve, Jiang, Tao, Kleinhofs, Andris, Muehlbauer, Gary J., Wise, Roger P., Stein, Nils, Ma, Yaqin, Rodriguez, Edmundo, Kudrna, Dave, Bhat, Prasanna R., Chao, Shiaoman, Condamine, Pascal, Heinen, Shane, Resnik, Josh, Wing, Rod, Witt, Heather N., Alpert, Matthew, Beccuti, Marco, Bozdag, Serdar, Cordero, Francesca, Mirebrahim, Hamid, Ounit, Rachid, Wu, Yonghui, You, Frank, Zheng, Jie, Simková, Hana, Dolezel, Jaroslav, Grimwood, Jane, Schmutz, Jeremy, Duma, Denisa, Altschmied, Lothar, Blake, Tom, Bregitzer, Phil, Cooper, Laurel, Dilbirligi, Muharrem, Falk, Anders, Feiz, Leila, Graner, Andreas, Gustafson, Perry, Hayes, Patrick M., Lemaux, Peggy, Mammadov, Jafar, and Close, Timothy J.
Abstract:: Barley (Hordeum vulgare L.) possesses a large and highly repetitive genome of 5.1 Gb that has hindered the development of a complete sequence. In 2012, the International Barley Sequencing Consortium released a resource integrating whole-genome shotgun sequences with a physical and genetic framework. However, because only 6278 bacterial artificial chromosome...
Resource Type:: Article
Full Text:: Sequencing of 15 622 gene-bearing BACs clarifies the

The Cobb hot spot: HIMU-DMM mixing and melting controlled by a progressively thinning lithospheric lid

Creator:: Chadwick, John, Keller, Randall, Kamenov, George, Yogodzinski, Gene, and Lupton, John
Abstract:: The Cobb Seamount Chain in the northeast Pacific basin records the composition of the Cobb hot spot for the past 33 Myr, as the migrating Juan de Fuca Ridge approached and ultimately overran it ca. 0.5 Myr ago. In this first comprehensive geochemical study of the Cobb chain, major and...
Resource Type:: Article
Full Text:: were collected during three R.V. Thomas Thompson cruises: Geochemistry, Geophysics, Geosystems 10.1002

Coding sequence density estimation via topological pressure

Creator:: Koslicki, David and Thompson, Daniel J.
Abstract:: We give a new approach to coding sequence (CDS) density estimation in genomic analysis based on the topological pressure, which we develop from a well known concept in ergodic theory. Topological pressure measures the ‘weighted information content’ of a finite word, and incorporates 64 parameters which can be interpreted as...
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Full Text:: pressure Coding sequence density estimation via topological pressure Koslicki, D., & Thompson, D. J

Experimental Methods to Study Gene Flow

Creator:: Mallory-Smith, Carol, Hall, Linda M., and Burgos, Nilda R.
Abstract:: Herbicide resistance is an exceptional marker to quantify gene flow. Quantification of pollen-, seed-, and vegetative propagule-mediated gene flow provides key weed biology information. Pollen-mediated gene flow influences the genetic variance within a population, the frequency of multiple or polygenic herbicide resistance, and the evolutionary dynamics of a species. Seed-mediated...
Resource Type:: Article
Full Text:: Experimental Methods to Study Gene Flow Experimental Methods

The effects of temperature and predator densities on the consumption of walleye pollock (Gadus chalcogrammus) by three groundfish in the Gulf of Alaska

Creator:: Thompson, Kevin A., Heppell, Selina S., and Thompson, Grant G.
Abstract:: Many multispecies models have assumed that prey density determines per-capita predator consumption rates, following a functional response relationship. However, empirical evidence suggests that a predator’s diet can also be influenced by a variety of environmental factors, including interactions with other predators. We used diet and abundance data from National Marine...
Resource Type:: Article
Full Text:: chalcogrammus) by three groundfish in the Gulf of Alaska Thompson, K. A., Heppell, S. S., & Thompson, G. G

Overexpression of thiamin biosynthesis genes increase leaf and seed thiamin content but not resistance to Xanthomonas oryzae in rice

Creator:: Dong, Wei, Thomas, Nicholas, Ronald, Pamela C., and Goyer, Aymeric
Abstract:: Thiamin diphosphate (ThDP), also known as vitamin B1, serves as an enzymatic cofactor in glucose metabolism, the Krebs cycle, and branched-chain amino acid biosynthesis in all living organisms. Unlike plants and microorganisms, humans are not able to synthesize ThDP de novo and must obtain it from their diet. Staple crops...
Resource Type:: Article
Full Text:: Accepted: 22 April 2016 Published: 10 May 2016 Citation: Dong W, Thomas N, Ronald PC and Goyer A (2016

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:: characterized plant pathogenic species. This type III effector gene conservation is particularly striking in the

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

Creator:: Vining, Kelly J., Pomraning, Kyle R., Wilhelm, Larry J., Priest, Henry D., Pellegrini, Matteo, Mockler, Todd C., Freitag, Michael, and Strauss, Steven H.
Abstract:: Background: DNA cytosine methylation is an epigenetic modification that has been implicated in many biological processes. However, large-scale epigenomic studies have been applied to very few plant species, and variability in methylation among specialized tissues and its relationship to gene expression is poorly understood. Results: We surveyed DNA methylation from...
Resource Type:: Article
Full Text:: methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Creator:: Nayfach, Stephen, Bradley, Patrick H., Wyman, Stacia K., Laurent, Timothy J., Williams, Alex, Eisen, Jonathan A., Pollard, Katherine S., and Sharpton, Thomas J.
Abstract:: Shotgun metagenomic DNA sequencing is a widely applicable tool for characterizing the functions that are encoded by microbial communities. Several bioinformatic tools can be used to functionally annotate metagenomes, allowing researchers to draw inferences about the functional potential of the community and to identify putative functional biomarkers. However, little is...
Resource Type:: Article
Full Text:: Automated and Accurate Estimation of Gene Family Abundance

Overexpression of Thiamin Biosynthesis Genes in Rice Increases Leaf and Unpolished Grain Thiamin Content But Not Resistance to Xanthomonas oryzae pv. oryzae

Creator:: Dong, Wei, Thomas, Nicholas, Ronald, Pamela C., and Goyer, Aymeric
Abstract:: Thiamin diphosphate (ThDP), also known as vitamin B1, serves as an enzymatic cofactor in glucose metabolism, the Krebs cycle, and branched-chain amino acid biosynthesis in all living organisms. Unlike plants and microorganisms, humans are not able to synthesize ThDP de novo and must obtain it from their diet. Staple crops...
Resource Type:: Article

ScholarsArchive@OSU

Sequencing of 15 622 gene-bearing BACs clarifies the gene-dense regions of the barley genome

The Cobb hot spot: HIMU-DMM mixing and melting controlled by a progressively thinning lithospheric lid

Coding sequence density estimation via topological pressure

Experimental Methods to Study Gene Flow

The effects of temperature and predator densities on the consumption of walleye pollock (Gadus chalcogrammus) by three groundfish in the Gulf of Alaska

Overexpression of thiamin biosynthesis genes increase leaf and seed thiamin content but not resistance to Xanthomonas oryzae in rice

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

Dynamic DNA cytosine methylation in the Populus trichocarpa genome: tissue-level variation and relationship to gene expression

Automated and Accurate Estimation of Gene Family Abundance from Shotgun Metagenomes

Overexpression of Thiamin Biosynthesis Genes in Rice Increases Leaf and Unpolished Grain Thiamin Content But Not Resistance to Xanthomonas oryzae pv. oryzae

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