Index Catalog // ScholarsArchive@OSU

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

Creator:: Koslicki, David, Chatterjee, Saikat, Shahrivar, Damon, Walker, Alan W., Francis, Suzanna C., Fraser, Louise J., Vehkaperä, Mikko, Lan, Yueheng, and Corander, Jukka
Abstract:: Motivation: Estimation of bacterial community composition from high-throughput sequenced 16S rRNA gene amplicons is a key task in microbial ecology. Since the sequence data from each sample typically consist of a large number of reads and are adversely impacted by different levels of biological and technical noise, accurate analysis of...
Resource Type:: Article
Full Text:: Community Composition. PLoS ONE, 10(10), e0140644. doi:10.1371/journal.pone.0140644 10.1371/journal.pone

Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders

Creator:: Kroll, Andrew J., Garcia, Tiffany S., Jones, Jay E., Dugger, Katie, Murden, Blake, Johnson, Josh, Peterman, Summer, Brintz, Ben, and Rochelle, Michael
Abstract:: Correction 23 Dec 2015: The PLOS ONE Staff (2015) Correction: Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders. PLOS ONE 10(12): e0145899. https://doi.org/10.1371/journal.pone.0145899
Resource Type:: Article

Theoretical Prediction of Disrupted Min Oscillation in Flattened Escherichia coli

Creator:: Schulte, Jeff B., Zeto, Rene W., and Roundy, David
Abstract:: The dynamics of the Min-protein system help Escherichia coli regulate the process of cell division by identifying the center of the cell. While this system exhibits robust bipolar oscillations in wild-type cell shapes, recent experiments have shown that when the cells are mechanically deformed into wide, flattened out, irregular shapes,...
Resource Type:: Article
Full Text:: Oscillation in Flattened Escherichia coli. PLoS ONE, 10(10), e0139813. doi:10.1371/journal.pone.0139813

Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P-humuli Using RNA Sequencing and Genotyping-By-Sequencing

Creator:: Summers, Carly F., Gulliford, Colwyn M., Carlson, Craig H., Lillis, Jacquelyn A., Carlson, Maryn O., Cadle-Davidson, Lance, Gent, David H., and Smart, Christine D.
Abstract:: RNA sequencing (RNA-seq) and genotyping-by-sequencing (GBS) were used for single nucleotide polymorphism (SNP) identification from two economically important obligate plant pathogens, Pseudoperonospora cubensis and P. humuli. Twenty isolates of P. cubensis and 19 isolates of P. humuli were genotyped using RNA-seq and GBS. Principle components analysis (PCA) of each data...
Resource Type:: Article
Full Text:: and Genotyping-By-Sequencing. PLoS ONE, 10(11), e0143665. doi:10.1371/journal.pone.0143665 10.1371

Flux Balance Analysis with Objective Function Defined by Proteomics Data-Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine

Creator:: Montezano, Daniel, Meek, Laura, Gupta, Rashmi, Bermudez, Luiz E., and Bermudez, José C. M.
Abstract:: We present a study of the metabolism of the Mycobacterium tuberculosis after exposure to antibiotics using proteomics data and flux balance analysis (FBA). The use of FBA to study prokaryotic organisms is well-established and allows insights into the metabolic pathways chosen by the organisms under different environmental conditions. To apply...
Resource Type:: Article
Full Text:: tuberculosis Exposed to Mefloquine. PLoS ONE, 10 (7), e0134014. doi:10.1371/journal.pone.0134014 10.1371

Redox Conductivity of Current-Producing Mixed Species Biofilms

Creator:: Li, Cheng, Lesnik, Keaton Larson, Fan, Yanzhen, and Liu, Hong
Abstract:: While most biological materials are insulating in nature, efficient extracellular electron transfer is a critical property of biofilms associated with microbial electrochemical systems and several microorganisms are capable of establishing conductive aggregates and biofilms. Though construction of these conductive microbial networks is an intriguing and important phenomenon in both natural...
Resource Type:: Article
Full Text:: | DOI:10.1371/journal.pone.0155247 May 9, 2016 1 / 14 a11111 OPEN ACCESS Citation: Li C, Lesnik KL

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

Creator:: Graebner, Ryan C., Wise, Mitchell, Cuesta-Marcos, Alfonso, Geniza, Matthew, Blake, Tom, Blake, Victoria C., Butler, Joshua, Chao, Shiaoman, Hole, David J., Horsley, Rich, Jaiswal, Pankaj, Obert, Don, Smith, Kevin P., Ullrich, Steven, and Hayes, Patrick M.
Abstract:: The Genome-Wide Association Studies approach was used to detect Quantitative Trait Loci associated with tocochromanol concentrations using a panel of 1,466 barley accessions. All major tocochromanol types- α-, β-, δ-, γ-tocopherol and tocotrienol- were assayed. We found 13 single nucleotide polymorphisms associated with the concentration of one or more of...
Resource Type:: Article
Full Text:: ) pathway in barley. PLoS ONE, 10(7), e0133767. doi:10.1371/journal.pone.0133767 10.1371/journal.pone

Is Western Diet-Induced Nonalcoholic Steatohepatitis in Ldlr(-/-) Mice Reversible?

Creator:: Lytle, Kelli A. and Jump, Donald B.
Abstract:: Background: Nonalcoholic fatty liver disease (NAFLD) is a major public health burden in western societies. The progressive form of NAFLD, nonalcoholic steatohepatitis (NASH), is characterized by hepatosteatosis, inflammation, oxidative stress, and hepatic damage that can progress to fibrosis and cirrhosis; risk factors for hepatocellular carcinoma. Given the scope of NASH,...
Resource Type:: Article
Full Text:: Ldlr(-/-) Mice Reversible?. PLoS ONE, 11(1), e0146942. doi:10.1371/journal.pone.0146942 10.1371

Geo-Referenced, Abundance Calibrated Ocean Distribution of Chinook Salmon (Oncorhynchus tshawytscha) Stocks across the West Coast of North America

Creator:: Bellinger, M. Renee, Banks, Michael A., Bates, Sarah J., Crandall, Eric D., Garza, John Carlos, Sylvia, Gil, and Lawson, Peter W.
Abstract:: Understanding seasonal migration and localized persistence of populations is critical for effective species harvest and conservation management. Pacific salmon (genus Oncorhynchus) forecasting models predict stock composition, abundance, and distribution during annual assessments of proposed fisheries impacts. Most models, however, fail to account for the influence of biophysical factors on year-to-year...
Resource Type:: Article
Full Text:: ONE, 10(7), e0131276. doi:10.1371/journal.pone.0131276 10.1371/journal.pone.0131276 Public Library

Evaluating Temporal Consistency in Marine Biodiversity Hotspots

Creator:: Piacenza, Susan E., Thurman, Lindsey L., Barner, Allison K., Benkwitt, Cassandra E., Boersma, Kate S., Cerny-Chipman, Elizabeth B., Ingeman, Kurt E., Kindinger, Tye L., Lindsley, Amy J., Nelson, Jake, Reimer, Jessica N., Rowe, Jennifer C., Shen, Chenchen, Thompson, Kevin A., and Heppell, Selina S.
Abstract:: With the ongoing crisis of biodiversity loss and limited resources for conservation, the concept of biodiversity hotspots has been useful in determining conservation priority areas. However, there has been limited research into how temporal variability in biodiversity may influence conservation area prioritization. To address this information gap, we present an...
Resource Type:: Article
Full Text:: Hotspots. PLoS ONE, 10(7), e0133301. doi:10.1371/journal.pone.0133301 10.1371/journal.pone.0133301

ScholarsArchive@OSU

ARK: Aggregation of Reads by K-Means for Estimation of Bacterial Community Composition

Evaluating Multi-Level Models to Test Occupancy State Responses of Plethodontid Salamanders

Theoretical Prediction of Disrupted Min Oscillation in Flattened Escherichia coli

Identification of Genetic Variation between Obligate Plant Pathogens Pseudoperonospora cubensis and P-humuli Using RNA Sequencing and Genotyping-By-Sequencing

Flux Balance Analysis with Objective Function Defined by Proteomics Data-Metabolism of Mycobacterium tuberculosis Exposed to Mefloquine

Redox Conductivity of Current-Producing Mixed Species Biofilms

Quantitative Trait Loci Associated with the Tocochromanol (Vitamin E) Pathway in Barley

Is Western Diet-Induced Nonalcoholic Steatohepatitis in Ldlr(-/-) Mice Reversible?

Geo-Referenced, Abundance Calibrated Ocean Distribution of Chinook Salmon (Oncorhynchus tshawytscha) Stocks across the West Coast of North America

Evaluating Temporal Consistency in Marine Biodiversity Hotspots

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