Index Catalog // ScholarsArchive@OSU

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:: Vibrio cholerae Yusuke Minato1, Sara R. Fassio2, Claudia C. Häse1,2* 1 Department of Biomedical

Isotopic constraints on the pre-industrial oceanic nitrogen budget

Creator:: Somes, C. J., Oschlies, A., and Schmittner, A.
Abstract:: The size of the bioavailable (i.e., “fixed”) nitrogen inventory in the ocean influences global marine productivity and the biological carbon pump. Despite its importance, the pre-industrial rates for the major source and sink terms of the oceanic fixed nitrogen budget, N₂ fixation and denitrification, respectively, are not well known. These...
Resource Type:: Article
Full Text:: nitrogen budget C. J. Somes1, A. Oschlies1, and A. Schmittner2 1GEOMAR Helmholtz-Zentrum f̈ur

Selenium Supplementation Restores Innate and Humoral Immune Responses in Footrot-Affected Sheep

Creator:: Hall, Jean A., Vorachek, William R., Stewart, Whitney C., Gorman, M. Elena, Mosher, Wayne D., Pirelli, Gene J., and Bobe, Gerd
Abstract:: Dietary selenium (Se) alters whole-blood Se concentrations in sheep, dependent upon Se source and dosage administered, but little is known about effects on immune function. We used footrot (FR) as a disease model to test the effects of supranutritional Se supplementation on immune function. To determine the effect of Se-source...
Resource Type:: Article
Full Text:: and Humoral Immune Responses in Footrot-Affected Sheep Jean A. Hall1*, William R. Vorachek1, Whitney C

Effect of Feeding Selenium-Fertilized Alfalfa Hay on Performance of Weaned Beef Calves

Creator:: Hall, Jean A., Bobe, Gerd, Hunter, Janice K., Vorachek, William R., Stewart, Whitney C., Vanegas, Jorge A., Estill, Charles T., Mosher, Wayne D., and Pirelli, Gene J.
Abstract:: Selenium (Se) is an essential micronutrient in cattle, and Se-deficiency can affect morbidity and mortality. Calves may have greater Se requirements during periods of stress, such as during the transitional period between weaning and movement to a feedlot. Previously, we showed that feeding Se-fertilized forage increases whole-blood (WB) Se concentrations...
Resource Type:: Article
Full Text:: , William R. Vorachek1, Whitney C. Stewart2¤b, Jorge A. Vanegas4, Charles T. Estill2,4, Wayne D. Mosher2

Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression

Creator:: Saldivar, Joshua C., Miuma, Satoshi, Bene, Jessica, Hosseini, Seyed Ali, Shibata, Hidetaka, Sun, Jin, Wheeler, Linda J., Mathews, Christopher K., and Huebner, Kay
Abstract:: Genomic instability drives tumorigenesis, but how it is initiated in sporadic neoplasias is unknown. In early preneoplasias, alterations at chromosome fragile sites arise due to DNA replication stress. A frequent, perhaps earliest, genetic alteration in preneoplasias is deletion within the fragile FRA3B/FHIT locus, leading to loss of Fhit protein expression....
Resource Type:: Article
Full Text:: Preneoplastic Processes through Loss of Fhit Expression Joshua C. Saldivar1,2, Satoshi Miuma2, Jessica Bene2

The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx): goals, platforms, and field operations

Creator:: Wood, R., Mechoso, C. R., Bretherton, C. S., Weller, R. A., Huebert, B., Straneo, F., Albrecht, B. A., Coe, H., Allen, G., Vaughan, G., Daum, P., Fairall, C., Chand, D., Klenner, L. Gallardo, Garreaud, R., Grados, C., Covert, D. S., Bates, T. S., Krejci, R., Russell, L. M., de Szoeke, Simon P., Brewer, A., Yuter, S. E., Springston, S. R., Chaigneau, A., Toniazzo, T., Minnis, P., Palikonda, R., Abel, S. J., Brown, W. O. J., Williams, S., Fochesatto, J., Brioude, J., and Bower, K. N.
Abstract:: The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx) was an international field program designed to make observations of poorly understood but critical components of the coupled climate system of the southeast Pacific. This region is characterized by strong coastal upwelling, the coolest SSTs in the tropical belt, and is home to...
Resource Type:: Article
Full Text:: , platforms, and field operations R. Wood1, C. R. Mechoso2, C. S. Bretherton1, R. A. Weller3, B. Huebert4, F

High-resolution glacial and deglacial record of atmospheric methane by continuous-flow and laser spectrometer analysis along the NEEM ice core

Creator:: Chappellaz, J., Stowasser, C., Blunier, T., Baslev-Clausen, D., Brook, Edward J., Dallmayr, R., Fain, X., Lee, J. E., Mitchell, L. E., Pascual, O., Romanini, D., Rosen, J., and Schuepbach, S.
Abstract:: The Greenland NEEM (North Greenland Eemian Ice Drilling) operation in 2010 provided the first opportunity to combine trace-gas measurements by laser spectroscopic instruments and continuous-flow analysis along a freshly drilled ice core in a field-based setting. We present the resulting atmospheric methane (CH₄) record covering the time period from 107.7...
Resource Type:: Article
Full Text:: ice core J. Chappellaz1,** , C. Stowasser2,** , T. Blunier2, D. Baslev-Clausen2, E. J. Brook3, R

A first chronology for the North Greenland Eemian Ice Drilling (NEEM) ice core

Creator:: Rasmussen, S. O., Abbott, P. M., Blunier, T., Bourne, A. J., Brook, Edward J., Buchardt, S. L., Buizert, Christo, Chappellaz, J., Clausen, H. B., Cook, E., Dahl-Jensen, D., Davies, S. M., Guillevic, M., Kipfstuhl, S., Laepple, T., Seierstad, I. K., Severinghaus, J. P., Steffensen, J. P., Stowasser, C., Svensson, A., Vallelonga, P., Vinther, B. M., Wilhelms, F., and Winstrup, M.
Abstract:: A stratigraphy-based chronology for the North Greenland Eemian Ice Drilling (NEEM) ice core has been derived by transferring the annual layer counted Greenland Ice Core Chronology 2005 (GICC05) and its model extension (GICC05modelext) from the NGRIP core to the NEEM core using 787 match points of mainly volcanic origin identified...
Resource Type:: Article
Full Text:: . M. Abbott2, T. Blunier1, A. J. Bourne2, E. Brook3, S. L. Buchardt1, C. Buizert3, J. Chappellaz4, H

In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

Creator:: Hicks, Kiley A., Howe, Dana K., Leung, Aubrey, Denver, Dee R., and Estes, Suzanne
Abstract:: In We have analyzed natural variation in mitochondrial form and function among a set of Caenorhabditis briggsae isolates known to harbor mitochondrial DNA structural variation in the form of a heteroplasmic nad5 gene deletion (nad5 Delta) that correlates negatively with organismal fitness. We performed in vivo quantification of 24 mitochondrial...
Resource Type:: Article
Full Text:: light of recent evidence for local adaptation to temperature in C. briggsae. Analysis of mitochondrial

Who supports the legalization of marijuana? The impact of liberalism and age on attitudes surrounding legalization of recreational marijuana

Creator:: Koll, Aiden
Abstract:: In an era of political polarization, the possibility of the legalization of recreational marijuana has become a popular topic of controversy. While a few states have passed general legislation, the vast majority still prohibit recreational use. In the interest of understanding why there are so many differences between the states,...
Resource Type:: Research Paper
Full Text:: –906. doi:10.1016/s2215-0366(16)30071-2. Lackey, Sara C. 2015. "The impact of age on political

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:: testing enrichment of a GO category. D �DD Sum C 1962 9803 11765 �CC 118 709 827 Sum 2080 10512 12592

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:: . Common: Earlier works of Robinson and Smyth [19] discussed a common dispersion model where f is a

Amino Acid Uptake in Arbuscular Mycorrhizal Plants

Creator:: Whiteside, Matthew D., Garcia, Maria O., and Treseder, Kathleen K.
Abstract:: We examined the extent to which arbuscular mycorrhizal (AM) fungi root improved the acquisition of simple organic nitrogen (ON) compounds by their host plants. In a greenhouse-based study, we used quantum dots (fluorescent nanoparticles) to assess uptake of each of the 20 proteinaceous amino acids by AM-colonized versus uncolonized plants....
Resource Type:: Article
Full Text:: Sciences 107: 13754–13759. 8. Paungfoo-Lonhienne C, Lonhienne TGA, Rentsch D, Robinson N, Christie M, et

Footprint of Positive Selection in Treponema pallidum subsp. pallidum Genome Sequences Suggests Adaptive Microevolution of the Syphilis Pathogen

Creator:: Giacani, Lorenzo, Chattopadhyay, Sujay, Centurion-Lara, Arturo, Jeffrey, BrendanM., Le, Hoavan T., Molini, Barbara J., Lukehart, Sheila A., Sokurenko, Evgeni V., and Rockey, Daniel D.
Abstract:: In the rabbit model of syphilis, infection phenotypes associated with the Nichols and Chicago strains of Treponema pallidum (T. pallidum), though similar, are not identical. Between these strains, significant differences are found in expression of, and antibody responses to some candidate virulence factors, suggesting the existence of functional genetic differences...
Resource Type:: Article
Full Text:: evenly split between C/T and A/G transitions and were not clustered, but distributed more or less evenly

Post-fire tree establishment and early cohort development in conifer forests of the western Cascades of Oregon, USA

Creator:: Tepley, Alan J., Swanson, Frederick J., and Spies, Thomas A.
Abstract:: Early‐seral ecosystems make important contributions to regional biodiversity by supporting high abundance and diversity of many plant and animal species that are otherwise rare or absent from closed‐canopy forests. Therefore, the period of post‐fire tree establishment is a key stage in forest stand and ecosystem development that can be viewed...
Resource Type:: Article
Full Text:: TEPLEY ET AL. ponderosa Douglas ex P. Lawson & C. Lawson) in drier regions. Fire-caused wounds that

Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

Creator:: Peterson, G. Jack, Pressé, Steve, Peterson, Kristin S., and Dill, Ken A.
Abstract:: We model the evolution of eukaryotic protein-protein interaction (PPI) networks. In our model, PPI networks evolve by two known biological mechanisms: (1) Gene duplication, which is followed by rapid diversification of duplicate interactions. (2) Neofunctionalization, in which a mutation leads to a new interaction with some other protein. Since many...
Resource Type:: Article
Full Text:: protein A can bind to proteins B and C, then there is a greater-than-random chance that B and C will

Predicting foundation bunchgrass species abundances: model-assisted decision-making in protected-area sagebrush steppe

Creator:: Rodhouse, Thomas J., Irvine, Kathryn M., Sheley, Roger L., Smith, Brenda S., Hoh, Shirley, Esposito, Daniel M., and Mata-Gonzalez, Ricardo
Abstract:: Foundation species are structurally dominant members of ecological communities that can stabilize ecological processes and influence resilience to disturbance and resistance to invasion. Being common, they are often overlooked for conservation but are increasingly threatened from land use change, biological invasions, and over‐exploitation. The pattern of foundation species abundances over...
Resource Type:: Article
Full Text:: . 2010. Analysis of ordinal categorical data. John Wiley and Sons, Hoboken, New Jersey, USA. Angelini, C

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:: approach is now being applied to eukary- otic model systems such as C. elegans and yeast [66–68]. These

A bioenergetics model to evaluate demographic consequences of disturbance in marine mammals applied to gray whales

Creator:: Villegas-Amtmann, S., Schwarz, L. K., Sumich, J. L., and Costa, D. P.
Abstract:: While sophisticated tools are used to monitor behavioral changes of large marine vertebrates, determining whether these changes are meaningful for management and conservation is challenging. The Population Consequences of Disturbance model proposed a bioenergetics model to detect biologically meaningful population responses, where disturbance costs are linked to lost energy. The...
Resource Type:: Article
Full Text:: March 2015; published 22 October 2015. Corresponding Editor: D. P. C. Peters. Copyright: � 2015

Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

Creator:: Winter, Christian, Payet, Jérôme P., and Suttle, Curtis A.
Abstract:: One of the challenges in oceanography is to understand the influence of environmental factors on the abundances of prokaryotes and viruses. Generally, conventional statistical methods resolve trends well, but more complex relationships are difficult to explore. In such cases, Artificial Neural Networks (ANNs) offer an alternative way for data analysis....
Resource Type:: Article
Full Text:: environment are distinctly different among the prokaryotic and viral populations. Citation: Winter C, Payet

ScholarsArchive@OSU

Malonate Inhibits Virulence Gene Expression in Vibrio cholerae

Isotopic constraints on the pre-industrial oceanic nitrogen budget

Selenium Supplementation Restores Innate and Humoral Immune Responses in Footrot-Affected Sheep

Effect of Feeding Selenium-Fertilized Alfalfa Hay on Performance of Weaned Beef Calves

Initiation of Genome Instability and Preneoplastic Processes through Loss of Fhit Expression

The VAMOS Ocean-Cloud-Atmosphere-Land Study Regional Experiment (VOCALS-REx): goals, platforms, and field operations

High-resolution glacial and deglacial record of atmospheric methane by continuous-flow and laser spectrometer analysis along the NEEM ice core

A first chronology for the North Greenland Eemian Ice Drilling (NEEM) ice core

In Vivo Quantification Reveals Extensive Natural Variation in Mitochondrial Form and Function in Caenorhabditis briggsae

Who supports the legalization of marijuana? The impact of liberalism and age on attitudes surrounding legalization of recreational marijuana

Length Bias Correction in Gene Ontology Enrichment Analysis Using Logistic Regression

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

Amino Acid Uptake in Arbuscular Mycorrhizal Plants

Footprint of Positive Selection in Treponema pallidum subsp. pallidum Genome Sequences Suggests Adaptive Microevolution of the Syphilis Pathogen

Post-fire tree establishment and early cohort development in conifer forests of the western Cascades of Oregon, USA

Simulated Evolution of Protein-Protein Interaction Networks with Realistic Topology

Predicting foundation bunchgrass species abundances: model-assisted decision-making in protected-area sagebrush steppe

Evolutionary Biology for the 21st Century

A bioenergetics model to evaluate demographic consequences of disturbance in marine mammals applied to gray whales

Modeling the Winter–to–Summer Transition of Prokaryotic and Viral Abundance in the Arctic Ocean

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