Digital Commons Network^™

Genome -Scale Reconstruction Of Metabolic Networks Of Lactobacillus Casei Atcc 334 And 12a, Elena Vinay-Lara, Joshua J. Hamilton, Buffy Stahl, Jeff Broadbent, Jennifer L. Reed, James L. Steele

Nutrition, Dietetics, and Food Sciences Faculty Publications

Lactobacillus casei strains are widely used in industry and the utility of this organism in these industrial applications is straindependent. Hence, tools capable of predicting strain specific phenotypes would have utility in the selection of strains forspecific industrial processes. Genome-scale metabolic models can be utilized to better understand genotype-phenotyperelationships and to compare different organisms. To assist in the selection and development of strains with enhancedindustrial utility, genome-scale models for L. casei ATCC 334, a well characterized strain, and strain 12A, a corn silage isolate,were constructed. Draft models were generated from RAST genome annotations using the Model SEED database and refined …

Between Two Fern Genomes, E. B. Sessa, J. A. Banks, M. S. Barker, J. P. Der, A. M. Duffy, S. W. Graham, M. Hasebe, J. Langdale, F. W. Li, D. B. Marchant, K. M. Pryer, C. J. Rothfels, S. J. Roux, M. L. Salmi, E. M. Sigel, D. E. Soltis, P. S. Soltis, D. W. Stevenson, Paul G. Wolf

Biology Faculty Publications

Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the …

Genotyping-By-Sequencing For Populus Population Genomics: An Assessment Of Genome Sampling Patterns And Filtering Approaches, M. Schilling, Paul G. Wolf, A. M. Duffy, H. S. Rai, C. A. Rowe, B. A. Richardson, K. E. Mock

Biology Faculty Publications

Continuing advances in nucleotide sequencing technology are inspiring a suite of genomic approaches in studies of natural populations. Researchers are faced with data management and analytical scales that are increasing by orders of magnitude. With such dramatic advances comes a need to understand biases and error rates, which can be propagated and magnified in large-scale data acquisition and processing. Here we assess genomic sampling biases and the effects of various population-level data filtering strategies in a genotyping-by-sequencing (GBS) protocol. We focus on data from two species of Populus, because this genus has a relatively small genome and is emerging …

A Samoan Hebeloma With Phylogenetic Ties To The Western Pacific, Bradley R. Kropp

Biology Faculty Publications

Hebeloma ifeleletorum is described as a new species from American Samoa. Based on analyses of ITS and combined nLSU-ITS datasets H. ifeleletorum clusters with but is distinct from described species that have been placed in the genus Anamika by some. The phylogenetic relationship of H. ifeleletorum to the genus Anamika from Asia and to other species from Australia and New Caledonia suggests that H. ifeleletorum has origins in the western Pacific.

Production Of Destruxins From Metarhizium Spp. Fungi In Artificial Medium And In Endophytically Colonized Cowpea Plants, P. S. Golo, D. R. Gardner, Michelle M. Grilley, Jon Y. Takemoto, S. B. Krasnoff, M. S. Pires, E. K. K. Férnandes, V. R. Bittencourt, Donald W. Roberts

Biology Faculty Publications

Destruxins (DTXs) are cyclic depsipeptides produced by many Metarhizium isolates that have long been assumed to contribute to virulence of these entomopathogenic fungi. We evaluated the virulence of 20 Metarhizium isolates against insect larvae and measured the concentration of DTXs A, B, and E produced by these same isolates in submerged (shaken) cultures. Eight of the isolates (ARSEF 324, 724, 760, 1448, 1882, 1883, 3479, and 3918) did not produce DTXs A, B, or E during the five days of submerged culture. DTXs were first detected in culture medium at 2–3 days in submerged culture. Galleria mellonella and Tenebrio molitor …

Water Resources Systems Analysis: A Bright Past And Challenging But Promising Future, David E. Rosenberg, Kaveh Madani

Civil and Environmental Engineering Faculty Publications

The field of water resources systems analysis is now experiencing one of its most exciting eras where scientists, decision makers, and funding agencies want to apply systems approaches to solve varied, complex, uncertain, and interdisciplinary resource management problems. Solving these problems presents great opportunities for us to engage in complex, real-world decision-making and make positive changes. However, to capitalize on these opportunities, we as a field must also overcome several large challenges related to problem identification, integration, blind use of systems tools, a focus on optimality, and harnessing big data. To overcome, we must look back to find what we …

A Shortcut For Multiple Testing On The Directed Acyclic Graph Of Gene Ontology, Garrett Saunders, John R. Stevens, S. Clay Isom

Mathematics and Statistics Faculty Publications

Background: Gene set testing has become an important analysis technique in high throughput microarray and next generation sequencing studies for uncovering patterns of differential expression of various biological processes. Often, the large number of gene sets that are tested simultaneously require some sort of multiplicity correction to account for the multiplicity effect. This work provides a substantial computational improvement to an existing familywise error rate controlling multiplicity approach (the Focus Level method) for gene set testing in high throughput microarray and next generation sequencing studies using Gene Ontology graphs, which we call the Short Focus Level.

Results: The Short Focus …

Adaptive Wetland Management In An Uncertain And Changing Arid Environment, Rebekah Downward, Joanna Endter-Wada, Karin M. Kettenring

Environment and Society Faculty Publications

Wetlands in the arid western United States provide rare and critical migratory bird habitat and constitute a critical nexus within larger social-ecological systems (SES) where multiple changing land-use and water-use patterns meet. The Bear River Migratory Bird Refuge in Utah, USA, presents a case study of the ways that wetland managers have created adaptive management strategies that are responsive to the social and hydrological conditions of the agriculture-dominated SES within which they are located. Managers have acquired water rights and constructed infrastructure while cultivating collaborative relationships with other water users to increase the adaptive capacity of the region and decrease …

Johne's Disease, Mycoplasma And Bvd In Utah - Bulk Tank Milk Testing And Comparison To Previous Regional Prevalence And Individual Herd Results Over Time, David J. Wilson, Kerry A. Rood, J. Bunnell, C. Whitehouse, G. M. Goodell, T. M. Byrem

Animal, Dairy, and Veterinary Science Faculty Publications

Dairy herd-level prevalence of Mycobacterium avium subsp. paratuberculosis (MAP), causative agent of Johne’s disease (JD), Mycoplasma spp., and Bovine Viral Diarrhea (BVD) virus were estimated in Utah and surrounding states and compared to previous surveillance results. Milk was collected at 3-4 day intervals on 5 dates (duplicate samples) from each bulk tank on participating farms, samples analyzed separately. One frozen sample was shipped to a laboratory for JD/MAP testing with ELISA and real-time PCR, the other paired sample was shipped to another laboratory for mycoplasma and BVD testing. Mycoplasma was cultured on modified Hayflick medium, standard methods; BVD testing was …

Russian Olive Control - Cut Stump Treatment, Ron Patterson, Dennis Worwood

All Current Publications

This fact sheet discusses cut stump herbicide treatment, which can be used to control Russian olive at any time of the year.

Nurturing Native Plants, A Guide To Vegetative Propagation Of Native Woody Plants In Utah, Larry Rupp, Adrea Wheaton

All Current Publications

The goal of this publication was to collect propagation protocols from research literature and compile successful methods used for each native species listed. Where information was unavailable for a species, we have listed the only propagation alternatives. The propagation protocols are laid out much like a recipe would be, listing the various ingredients and materials required for each ‘dish’. This ‘cookbook’ is a work-in-progress. If you find you have additions to suggest, please email: [email protected].

Utah Vegetable Production And Pest Management Guide 2014, Utah State University Extension

All Current Publications

No abstract provided.

Practicing Environmental Etiquette In Utah's Deserts, Jordan Burningham

All Current Publications

World-renown for its desert climate and recreational opportunities, Utah’s southern desert attracts millions of visitors each year. With nearly 75% of the land in Utah being public[1], much of it is dedicated to recreation and tourism in the form of National Parks, Monuments, National Forests and open space.

A Tree-Ring Based Reconstruction Of Logan River Streamflow In Northern Utah, Eric B. Allen, Tammy M. Rittenour, R. Justin Derose, Matthew F. Bekker, Roger Kjelgren, Brendan M. Buckley

Wasatch Dendroclimatology Research

[1] We created six new tree-ring chronologies in northern Utah, which were used with preexisting chronologies from Utah and western Wyoming to reconstruct mean annual flow for the Logan River, the largest tributary of the regionally important Bear River. Two reconstruction models were developed, a “Local” model that incorporated two Rocky Mountain juniper chronologies located within the basin, and a “Regional” model that also included limber pine and pinyon pine chronologies from a larger area. The Local model explained 48.2% of the variability in the instrumental record and the juniper chronologies better captured streamflow variability than Douglas-fir collected within the …

A Tree-Ring Based Reconstruction Of Logan River Streamflow, Northern Utah, Eric B. Allen, Tammy M. Rittenour, R. Justin Derose, Matthew F. Bekker, Roger Kjelgren, Brendan M. Buckley

Geosciences Faculty Publications

We created six new tree‐ring chronologies in northern Utah, which were used with preexisting chronologies from Utah and western Wyoming to reconstruct mean annual flow for the Logan River, the largest tributary of the regionally important Bear River. Two reconstruction models were developed, a “Local” model that incorporated two Rocky Mountain juniper chronologies located within the basin, and a “Regional” model that also included limber pine and pinyon pine chronologies from a larger area. The Local model explained 48.2% of the variability in the instrumental record and the juniper chronologies better captured streamflow variability than Douglas‐fir collected within the Logan …

The Influence Of Snowmobile Trails On Coyote Movements During Winter In High-Elevation Landscapes, Eric M. Gese, Jennifer L. Burghardt Dowd, Lise M. Aubry

Wildland Resources Faculty Publications

Competition between sympatric carnivores has long been of interest to ecologists. Increased understanding of these interactions can be useful for conservation planning. Increased snowmobile traffic on public lands and in habitats used by Canada lynx (Lynx canadensis) remains controversial due to the concern of coyote (Canis latrans) use of snowmobile trails and potential competition with lynx. Determining the variables influencing coyote use of snowmobile trails has been a priority for managers attempting to conserve lynx and their critical habitat. During 2 winters in northwest Wyoming, we backtracked coyotes for 265 km to determine how varying snow characteristics influenced coyote movements; …

Faith And Doubt As Partners In Mormon History, Gregory A. Prince

Arrington Annual Lecture

No abstract provided.

Faculty Senate Executive Committee Agenda, December 9, 2013, Utah State University

Faculty Senate & Faculty Senate Executive Committee

• Word change in 402.4.3 (Second Reading) - Stephen Bialkowski
• Word change in 405.6 (Second Reading) - Stephen Bialkowski
• Word change from ASUSU to USUSA all 400 sections (Second Reading) - Stephen Bialkowski
• Discussion of code revision to 405.12 Post-Tenure Review Process - Renee Galligher

The Utah Statesman, December 5, 2013, Utah State University

The Utah Statesman

Weekly student newspaper of Utah State University in Logan.

Educational Policies Committee Minutes, December 5, 2013, Utah State University

Educational Policies Committee

• Subcommittee Reports
• Curriculum Subcommittee
• Academic Standards Subcommittee
• General Education Subcommittee

Educational Policies Committee Agenda, December 5, 2013, Utah State University

Educational Policies Committee

• Subcommittee Reports
• Curriculum Subcommittee
• Course Approvals
• Academic Standards Subcommittee
• General Education Subcommittee

Curriculum Subcommittee Agenda, December 5, 2013, Utah State University

Educational Policies Committee

Department of Applied Economics

• Prerequisite Change

School of Applied Sciences, Technology and Education

• New Course

Department of Nutrition, Dietetics and Food Sciences

• Course Description Change

Department of Plants, Soils and Climate

• Prerequisite Change

Department of Art and Design

• Title Change, Course Description Change
• Title Change, Credit Hour Change, Prerequisite Change, Remove Repeatable for Credit, Course Description Change
• Title Change, Credit Hour Change, Course Description Change
• Prerequisite Change

Jon M. Huntsman School of Business

• Title Change, Prerequisite Change, Course Description Change

Department of Management

• New Course
• Prerequisite Change, Course Description Change

Department of Health, Physical Education and Recreation

• New Course
• Course …

Curriculum Subcommittee Minutes, December 5, 2013, Utah State University

Educational Policies Committee

Department of Applied Economics

• Prerequisite Change

School of Applied Sciences, Technology and Education

• New Course

Department of Nutrition, Dietetics and Food Sciences

• Course Description Change

Department of Plants, Soils and Climate

• Prerequisite Change

Department of Art and Design

• Title Change, Course Description Change
• Title Change, Credit Hour Change, Prerequisite Change, Remove Repeatable for Credit, Course Description Change
• Title Change, Credit Hour Change, Course Description Change
• Prerequisite Change

Jon M. Huntsman School of Business

• Title Change, Prerequisite Change, Course Description Change

Department of Management

• New Course
• Prerequisite Change, Course Description Change

Department of Health, Physical Education and Recreation

• New Course
• Course …

The Utah Statesman, December 3, 2013, Utah State University

The Utah Statesman

Weekly student newspaper of Utah State University in Logan.

Creating Tomorrow, Fall 2013, College Of Engineering

College of Engineering Magazines

Annual magazine for the College of Engineering at Utah State University.

Permaculture, Roslynn Brain, Blake Thomas

Environment and Society Faculty Publications

No abstract provided.

Effect Of Predator Removal On Greater Sage-Grouse (Centrocercus Urophasianus) Ecology In The Bighorn Basin Conservation Area Of Wyoming, Elizabeth Kari Orning

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

The decline of greater sage-grouse distribution and population densities across western North America has led conservation, research, and management objectives to focus efforts on understanding sage-grouse populations across their range. The purpose of this study was to gain a better understanding of direct and indirect predation effects on hen survival and nest success of sage-grouse. The project was conducted in Hot Springs and Park Counties in the Bighorn Basin of Wyoming. The study had three main objectives: 1) obtain and quantify the types and impacts of predators on sage-grouse hen survival and nest success, 2) compare the effect predator removals …

Determination Of The Expression Patterns Of Bovine Non-Classical Major Histocompatibility Complex (Mhc) Class I Proteins, Parveen Parasar

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

This project was funded by the United States of Department of Agriculture (USDA), which funds research aimed at improving production and animal health. The aim of this study was to advance knowledge of maternal immune tolerance to the fetus and mechanisms bovine non-classical MHC class I proteins employ to interact with immune cells and render them inert towards the fetus.

A fetus is a tissue graft inside the mother’s uterus yet must be accepted by the mother to maintain a successful pregnancy. Reproductive insufficiency and pregnancy failure are major causes of production loss in cattle, especially in cloned animals. Knowledge …

An Algorithm To Recognize Multi-Stable Behavior From An Ensemble Of Stochastic Simulation Runs, Eduardo Monzon

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Synthetic biological designers are demanding tools to help with the design and verification process of new biological models. Some of the most common tools available aggregate multiple simulation results into one “clean” trajectory that hopefully is representative of the system’s behavior. However, for systems exhibiting multiple stable states, these techniques fail to show all the possible trajectories of the system. This work introduces a method capable of detecting the presence of more than one “typical” trajectory in a system, which can also be integrated with other available simulation tools.

Constraints On Patterns Of Abundance And Aggregation In Biological Systems, Kenneth J. Locey

All Graduate Theses and Dissertations, Spring 1920 to Summer 2023

Understanding the mechanisms that structure biological systems is a primary goal of biology. My research shows that the biological structure is constrained in important ways by general variables such as the number of base pairs in a genome and the number of individuals and species in a community. I used a combination of macroecology, bioinformatics, statistics, mathematics, and advanced computing to pursue my research and published several peer-reviewed scientific manuscripts and open-source software as a result.

I was funded through a combination of fellowships and scholarships awarded by the Utah State University School of Graduate Studies, College of Science, and …