Index Catalog // ScholarsArchive@OSU

Evolutionary Biology for the 21st Century

Creator:: Losos, Jonathan B., Arnold, Stevan J., Bejerano, Gill, Brodie, E. D. III, Hibbett, David, Hoekstra, Hopi E., Mindell, David P., Monteiro, Antonia, Moritz, Craig, Orr, H. Allen, Petrov, Dmitri A., Renner, Susanne S., Ricklefs, Robert E., Soltis, Pamela S., and Turner, Thomas L.
Abstract:: We live in an exciting time for biology. Technological advances have made data collection easier and cheaper than we could ever have imagined just 10 years ago. We can now synthesize and analyze large data sets containing genomes, transcriptomes, proteomes, and multivariate phenotypes. At the same time, society's need for...
Resource Type:: Article
Full Text:: , California, United States of America, 13 Department of Biology, University of Munich, Munich, Germany, 14

Malonate Inhibits Virulence Gene Expression in Vibrio cholerae

Creator:: Minato, Yusuke, Fassio, Sara R., and Häse, Claudia C.
Abstract:: We previously found that inhibition of the TCA cycle, either through mutations or chemical inhibition, increased toxT transcription in Vibrio cholerae. In this study, we found that the addition of malonate, an inhibitor of succinate dehydrogenase (SDH), decreased toxT transcription in V. cholerae, an observation inconsistent with the previous pattern...
Resource Type:: Article
Full Text:: 13, 2013 Copyright: � 2013 Minato et al. This is an open-access article distributed under the terms

Mechanistic Insights into Validoxylamine A 7’-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex

Creator:: Cavalier, Michael C., Yim, Young-Sun, Asamizu, Shumpei, Neau, David, Almabruk, Khaled H., Mahmud, Taifo, and Lee, Yong-Hwan
Abstract:: The pseudo-glycosyltransferase VldE catalyzes non-glycosidic C-N coupling between an unsaturated cyclitol and a saturated aminocyclitol with the conservation of the stereochemical configuration of the substrates to form validoxylamine A 7'-phosphate, the biosynthetic precursor of the antibiotic validamycin A. To study the molecular basis of its mechanism, the three-dimensional structures of...
Resource Type:: Article
Full Text:: Instrumentation, Russian Federation Received May 21, 2012; Accepted August 10, 2012; Published September 13, 2012

3,3'-Diindolylmethane Induces G₁ Arrest and Apoptosis in Human Acute T-Cell Lymphoblastic Leukemia Cells

Creator:: Shorey, Lyndsey E., Hagman, Amanda M., Williams, David E., Ho, Emily, Dashwood, Roderick H., and Benninghoff, Abby D.
Abstract:: Certain bioactive food components, including indole-3-carbinol (I3C) and 3,3'-diindolylmethane (DIM) from cruciferous vegetables, have been shown to target cellular pathways regulating carcinogenesis. Previously, our laboratory showed that dietary I3C is an effective transplacental chemopreventive agent in a dibenzo[def,p]chrysene (DBC)-dependent model of murine T-cell lymphoblastic lymphoma. The primary objective of the...
Resource Type:: Article
Full Text:: pone.0034975 1..13 3,39-Diindolylmethane Induces G1 Arrest and

The Level of Residual Dispersion Variation and the Power of Differential Expression Tests for RNA-Seq Data

Creator:: Mi, Gu and Di, Yanming
Abstract:: RNA-Sequencing (RNA-Seq) has been widely adopted for quantifying gene expression changes in comparative transcriptome analysis. For detecting differentially expressed genes, a variety of statistical methods based on the negative binomial (NB) distribution have been proposed. These methods differ in the ways they handle the NB nuisance parameters (i.e., the dispersion...
Resource Type:: Article
Full Text:: normalization can be incorporated into the GLM framework as well. See [13–15] for relevant discussions. DE

Roles of brca2 (fancd1) in Oocyte Nuclear Architecture, Gametogenesis, Gonad Tumors, and Genome Stability in Zebrafish

Creator:: Rodriguez-Mari, Adriana, Wilson, Catherine, Titus, Tom A., Canestro, Cristian, BreMiller, Ruth A., Yan, Yi-Lin, Nanda, Indrajit, Johnston, Adam, Kanki, John P., Gray, Erin M., He, Xinjun, Spitsbergen, Jan, Schindler, Detlev, and Postlethwait, John H.
Abstract:: Mild mutations in BRCA2 (FANCD1) cause Fanconi anemia (FA) when homozygous, while severe mutations cause common cancers including breast, ovarian, and prostate cancers when heterozygous. Here we report a zebrafish brca2 insertional mutant that shares phenotypes with human patients and identifies a novel brca2 function in oogenesis. Experiments showed that...
Resource Type:: Article
Full Text:: with conserved synteny to the orthologous region on human chromosome 13 (Hsa13, Figure 1A middle), as

Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage

Creator:: Bonito, Gregory, Smith, Matthew E., Nowak, Michael, Healy, Rosanne A., Guevara, Gonzalo, Cazares, Efren, Kinoshita, Akihiko, Nouhra, Eduardo R., Domınguez, Laura S., Tedersoo, Leho, Murat, Claude, Wang, Yun, Arroyo Moreno, Baldomero, Pfister, Donald H., Nara, Kazuhide, Zambonelli, Alessandra, Trappe, James M., and Vilgalys, Rytas
Abstract:: Truffles have evolved from epigeous (aboveground) ancestors in nearly every major lineage of fleshy fungi. Because accelerated rates of morphological evolution accompany the transition to the truffle form, closely related epigeous ancestors remain unknown for most truffle lineages. This is the case for the quintessential truffle genus Tuber, which includes...
Resource Type:: Article
Full Text:: Dipartimento di Science Agrarie, Università di Bologna, Bologna, Italy, 13 Institute of Systematic Botany

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

Creator:: Sim, Sung-Chur, Van Deynze, Allen, Stoffel, Kevin, Douches, David S., Zarka, Daniel, Ganal, Martin W., Chetelat, Roger T., Hutton, Samuel F., Scott, John W., Gardner, Randolph G., Panthee, Dilip R., Mutschler, Martha, Myers, James R., and Francis, David M.
Abstract:: The effects of selection on genome variation were investigated and visualized in tomato using a high-density single nucleotide polymorphism (SNP) array. 7,720 SNPs were genotyped on a collection of 426 tomato accessions (410 inbreds and 16 hybrids) and over 97% of the markers were polymorphic in the entire collection. Principal...
Resource Type:: Article

Palaeo-sea-level and palaeo-ice-sheet databases: problems, strategies, and perspectives

Creator:: Düsterhus, André, Rovere, Alessio, Carlson, Anders E., Horton, Benjamin P., Klemann, Volker, Tarasov, Lev, Barlow, Natasha L. M., Bradwell, Tom, Clark, Jorie, Dutton, Andrea, Gehrels, W. Roland, Hibbert, Fiona D., Hijma, Marc P., Khan, Nicole, Kopp, Robert E., Sivan, Dorit, and Törnqvist, Torbjörn E.
Abstract:: Sea-level and ice-sheet databases have driven numerous advances in understanding the Earth system. We describe the challenges and offer best strategies that can be adopted to build self-consistent and standardised databases of geological and geochemical information used to archive palaeo-sea-levels and palaeo-ice-sheets. There are three phases in the development of...
Resource Type:: Article
Full Text:: Development of a Sea- Level Database for Ireland, Irish J. Earth Sci., 24, 13–27, doi:10.3318/ijes

Factors affecting female space use in ten populations of prairie chickens

Creator:: Winder, Virginia L., Carrlson, Kaylan M., Gregory, Andrew J., Hagen, Christian A., Haukos, David A., Kesler, Dylan C., Larsson, Lena C., Matthews, Ty W., McNew, Lance B., Patten, Michael A., Pitman, Jim C., Powell, Larkin A., Smith, Jennifer A., Thompson, Tom, Wolfe, Donald H., and Sandercock, Brett K.
Abstract:: Conservation of wildlife depends on an understanding of the interactions between animal movements and key landscape factors. Habitat requirements of wide-ranging species often vary spatially, but quantitative assessment of variation among replicated studies at multiple sites is rare. We investigated patterns of space use for 10 populations of two closely...
Resource Type:: Article
Full Text:: /licenses/by/3.0/ 13 Present address: Ducks Unlimited, Bismarck, North Dakota 58503 USA. 14 Present address

ScholarsArchive@OSU

Evolutionary Biology for the 21st Century

Malonate Inhibits Virulence Gene Expression in Vibrio cholerae

Mechanistic Insights into Validoxylamine A 7’-Phosphate Synthesis by VldE Using the Structure of the Entire Product Complex

3,3'-Diindolylmethane Induces G₁ Arrest and Apoptosis in Human Acute T-Cell Lymphoblastic Leukemia Cells

The Level of Residual Dispersion Variation and the Power of Differential Expression Tests for RNA-Seq Data

Roles of brca2 (fancd1) in Oocyte Nuclear Architecture, Gametogenesis, Gonad Tumors, and Genome Stability in Zebrafish

Historical Biogeography and Diversification of Truffles in the Tuberaceae and Their Newly Identified Southern Hemisphere Sister Lineage

High-Density SNP Genotyping of Tomato (Solanum lycopersicum L.) Reveals Patterns of Genetic Variation Due to Breeding

Palaeo-sea-level and palaeo-ice-sheet databases: problems, strategies, and perspectives

Factors affecting female space use in ten populations of prairie chickens

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