Digital Commons Network^™

Atsubp-2.0: An Integrated Web Server For The Annotation Of Arabidopsis Proteome Subcellular Localization Using Deep Learning, Naveen Duhan, Rakesh Kaundal

Plants, Soils and Climate Student Research

The organization of subcellular components in a cell is critical for its function and studying cellular processes, protein–protein interactions, identifying potential drug targets, network analysis, and other systems biology mechanisms. Determining protein localization experimentally is time-consuming and expensive. Due to the need for meticulous experimentation, validation, and data analysis, computational methods provide a quick and accurate alternative. Arabidopsis thaliana, a beneficial model organism in plant biology, facilitates experimentation and applies to other plants. Predicting its proteins' subcellular localization can improve our understanding of cellular processes and have applications in crop improvement and biotechnology. We propose AtSubP-2.0, an extension of …

Same Data, Different Analysts: Variation In Effect Sizes Due To Analytical Decisions In Ecology And Evolutionary Biology, Elliot Gould, Hannah S. Fraser, Timothy H. Parker, Shinichi Nakagawa, Simon C. Griffith, Peter A. Vesk, Fiona Fidler, Daniel G. Hamilton, Robin N. Abbey-Lee, Jessica K. Abbott, Erica F. Stuber, Et Al.

Wildland Resources Faculty Publications

Although variation in effect sizes and predicted values among studies of similar phenomena is inevitable, such variation far exceeds what might be produced by sampling error alone. One possible explanation for variation among results is differences among researchers in the decisions they make regarding statistical analyses. A growing array of studies has explored this analytical variability in different fields and has found substantial variability among results despite analysts having the same data and research question. Many of these studies have been in the social sciences, but one small “many analyst” study found similar variability in ecology. We expanded the scope …

Starting Vegetable Seeds Indoors: I. Planning, Wesley Crump, Taun Beddes, Michael Caron, Milena Oliveira

All Current Publications

For many Utah gardeners, starting vegetable seeds indoors offers both an exciting opportunity to experiment with new varieties and a practical necessity for ensuring the successful growth and production of certain crops in their unique environmental conditions. Vegetable gardening involves inherent risks, particularly for the plants, with weather being a significant and largely uncontrollable factor. Because of this, many gardeners are unsure about when to start certain crops and whether the crops should be started indoors or sown directly in the garden. This fact sheet, the first in a series of four, discusses planning considerations when starting seeds indoors.

Determining Spatial Responses Of Fishers (Pakania Pennanti) To Mechanical Treatments Of Forest Stands For Fuel Reduction, Tessa R. Smith, Eric M. Gese, R. David Clayton, Patricia A. Terletzky, Kathryn L. Purcell, Craig M. Thompson

Wildland Resources Faculty Publications

Historical forestry practices (e.g., fire suppression, heavy timber logging) have contributed to a discernable change in stand composition of western forests in the U.S., which now comprise a tinderbox mixture of increased surface and ladder fuels, dense stands, and fire-intolerant species. Forest managers are mitigating this concern by implementing silviculture practices (e.g., selective logging, thinning, prescribed burning) to reduce fuel loads and improve stand resiliency. Concern for habitat specialists, such as the fisher (Pekania pennanti), have arisen as they may be negatively influenced in the short-term by modifications to their environment that are needed to ensure long-term habitat …

Lake Powell Fish Sampling: Glen Canyon Dam Forebay Area, 2022 And 2023, Phaedra Budy, Casey Pennock

Browse all Datasets

Native fishes face imperilment due to habitat loss and fragmentation, megadrought, invasive species, and synergies amongst threats. These threats coalesce at Glen Canyon Dam (GCD), which impounds the Colorado River to create Lake Powell, a reservoir inhabited by a suite of nonnative fishes. Water level in Lake Powell has declined precipitously due to water overallocation and megadrought, increasing the risk of nonnative fish entrainment through the dam, as the penstocks draw water from the epilimnion. Our goal was to characterize the distribution and abundance of nonnative fishes in the vicinity of GCD and identify environmental conditions that may increase entrainment. …

Impacts Of Changing Temperatures On The Water Budget In The Great Salt Lake Basin, Grace Affram, Jihad Othman, Reza Morovati, Saddy Pineda Castellanos, Sajad Khoshnoodmotlagh, Diana Dunn, Braedon Dority, Katherine Osorio Diaz, Cody Ratterman, Wei Zhang

Plants, Soils and Climate Student Research

Quantifying the water budget in the Great Salt Lake (GSL) basin is a nontrivial task, especially under a changing climate that contributes to increasing temperatures and a shift towards more rainfall and less snowfall. This study examines the potential impacts of temperature thresholds on the water budget in the GSL, emphasizing the influence on snowmelt, evapotranspiration (ET), and runoff under varying climate warming scenarios. Current hydrological models such as the Variable Infiltration Capacity (VIC) model use a universal temperature threshold to partition snowfall and rainfall across different regions. Previous studies have argued that there is a wide range of thresholds …

Tremblings, February 2025, Western Aspen Alliance

Tremblings

Bridging Conservation Science With Native Meaning

James Calabaza, Indigenous Lands Director; Trees, Water & People

Last fall, I had the privilege of collaborating with the Western Aspen Alliance and other partners to carry out a 3-day workshop focused on quaking aspen genetics, fire ecology, and co-stewardship. Held at Rocky Mountain Biological Laboratory (Gothic, Colorado), the workshop brought together academics, NGOs, federal agencies, and Tribal members to share diverse perspectives on aspen's significance and management futures.

Product Testing: Research Shows Benefits Of Biostimulants May Vary By Variety, Prakriti Nepal, Youping Sun, Milena Oliveira

Plants, Soils and Climate Student Research

The use of plant biostimulants is showing some promise as a potential means of helping onion crops thrive despite certain environmental challenges, according to new research at Utah State University.

Plasmids Encode And Can Mobilize Onion Pathogenicity In Pantoea Agglomerans, Gi Yoon Shin, Jo Ann Asselin, Amy Smith, Brenna Aegerter, Teresa Coutinho, Mei Zhao, Bhabesh Dutta, Jennie Mazzone, Ram Neupane, Beth Gugino, Christy Hoepting, Manzeal Khanal, Subas Malla, Claudia Nischwitz, Jaspreet Sidhu, Antoinette Machado Burke, Jane Davey, Mark Uchanski, Michael L. Derie, Lindsey J. Du Toit, Stephen Stresow-Cortez, Jean M. Bonasera, Paul Stodghill, Brian Kvitko

Biology Faculty Publications

Pantoea agglomerans is one of four Pantoea species reported in the USA to cause bacterial rot of onion bulbs. However, not all P. agglomerans strains are pathogenic to onion. We characterized onion-associated strains of P. agglomerans to elucidate the genetic and genomic signatures of onion-pathogenic P. agglomerans. We collected > 300 P. agglomerans strains associated with symptomatic onion plants and bulbs from public culture collections, research laboratories, and a multi-year survey in 11 states in the USA. Combining the 87 genome assemblies with 100 high-quality, public P. agglomerans genome assemblies we identified two well-supported P. agglomerans phylogroups. Strains causing severe …

Microbiome Metabolic Capacity Is Buffered Against Phylotype Losses By Functional Redundancy, Kayla Cross, Noelle Beckman, Benjamin Jahnes, Zakee L. Sabree

Biology Faculty Publications

Many animals contain a species-rich and diverse gut microbiota that likely contributes to several host-supportive services that include diet processing and nutrient provisioning. Loss of microbiome taxa and their associated metabolic functions as result of perturbations may result in loss of microbiome-level services and reduction of metabolic capacity. If metabolic functions are shared by multiple taxa (i.e., functional redundancy), including deeply divergent lineages, then the impact of taxon/function losses may be dampened. We examined to what degree alterations in phylotype diversity impact microbiome-level metabolic capacity. Feeding two nutritionally imbalanced diets to omnivorous Periplaneta americana over 8 weeks reduced the diversity …

Spatiotemporal Patterns Of Chlorophyll-A Concentration In A Hypersaline Lake Using High Temporal Resolution Remotely Sensed Imagery, R. Douglas Ramsey, Soren M. Brothers, Melissa Cobo, Wayne A. Wurtsbaugh

Wildland Resources Faculty Publications

The Great Salt Lake (GSL) is the largest saline lake in the Western Hemisphere. It supports billion-dollar industries and recreational activities, and is a vital stopping point for migratory birds. However, little is known about the spatiotemporal variation of phytoplankton biomass in the lake that supports these resources. Spectral reflectance provided by three remote sensing products was compared relative to their relationship with field measurements of chlorophyll a (Chl a). The MODIS product MCD43A4 with a 500 m spatial resolution provided the best overall ability to map the daily distribution of Chl a. The imagery indicated significant spatial …

Quantifying Dust Nutrient Mobility Through An Alpine Watershed, Jeffrey R. Nielson, Janice Brahney

Watershed Sciences Faculty Publications

Dust has the potential to play a significant role in the nutrient dynamics of alpine watersheds with important ecological implications. However, little is known about how dust nutrients circulate through the environment and which watershed characteristics facilitate dust impacts on water quality. This study explored the contribution of dust-deposited nutrients, focusing on a high-elevation Long Term Ecological Research site, where dust samples have been continuously collected since 2017. We incorporated observed dust nutrient compositions, including fractions of inorganic and organic nitrogen and phosphorus, into a popular hydrological model, the Soil and Water Assessment Tool, and ran simulations for 2019–2021. By …

Proximal Remote Sensing: An Essential Tool For Bridging The Gap Between High-Resolution Ecosystem Monitoring And Global Ecology, Zoe Amie Pierrat, Troy S. Magney, Will P. Richardson, Benjamin R. K. Runkle, Jen L. Diehl, Xi Yang, William Woodgate, William K. Smith, Miriam R. Johnston, Yohanes R. S. Ginting, Gerbrand Koren, Loren P. Albert, Christopher L. Kibler, Bryn E. Morgan, Mallory Barnes, Adriana Uscanga, Charles Devine, Mostafa Javadian, Karem Meza, Tommaso Julitta, Giulia Tagliabue, Matthew P. Dannenberg, Michal Antala, Christopher Y. S. Wong, Andre L. D. Santos, Koen Hufkens, Julia K, Marrs, Atticus E. L. Stovall, Yujie Liu, Joshua B. Fisher, John A. Gamon, Kerry Cawse-Nicholson

Civil and Environmental Engineering Student Research

A new proliferation of optical instruments that can be attached to towers over or within ecosystems, or ‘proximal’ remote sensing, enables a comprehensive characterization of terrestrial ecosystem structure, function, and fluxes of energy, water, and carbon. Proximal remote sensing can bridge the gap between individual plants, site-level eddy-covariance fluxes, and airborne and spaceborne remote sensing by providing continuous data at a high-spatiotemporal resolution. Here, we review recent advances in proximal remote sensing for improving our mechanistic understanding of plant and ecosystem processes, model development, and validation of current and upcoming satellite missions. We provide current best practices for data availability …

The Utah Statesman, January 20, 2025, Utah State University

The Utah Statesman

Weekly student newspaper of Utah State University in Logan.

Timber Harvesting Was The Most Important Factor Driving Changes In Vegetation Composition, As Compared To Climate And Fire Regime Shifts, In The Mixedwood Temperate Forests Of Temiscamingue Since Ad 1830, Daniela Robles, Yan Boulanger, Jesus Pascual, Victor Danneyrolles, Yves Bergeron, Igor Drobyshev

Aspen Bibliography

Context The vegetation composition of northeastern North American forests has significantly changed since pre-settlement times, with a marked reduction in conifer-dominated stands, taxonomic and functional diversity. These changes have been attributed to fire regime shifts, logging, and climate change.

Methods In this study, we disentangled the individual effects of these drivers on the forest composition in southwestern Quebec from 1830 to 2000 by conducting retrospective modelling using the LANDIS-II forest landscape model. The model was run based on pre-settlement forest composition and fire history reconstructions, historical timber harvest records, and climate reanalysis data. We compared counterfactual scenarios excluding individual factors …

A Comprehensive Parcel-Level Dataset On Farmland Assessment: Addressing Grid-Cell Data Bias Estimation, Wai Yan Siu, Man Li, Arthur J. Caplan

Applied Economics Faculty Publications

Grid-cell data are increasingly used in research due to the growing availability and accessibility of remote sensing products. However, grid-cell data often fails to represent the actual decision-making unit, leading to biased estimates in socio-economic analysis. To this end, this paper presents a comprehensive parcel-level dataset for Salt Lake County, Utah, spanning from 2008 to 2018. This dataset combines detailed spatial and temporal data on land ownership, land use, and preferential farmland tax assessments under the Greenbelt program. Compiled from multiple geospatial sources, the dataset includes nearly 200,000 parcel-year observations, providing valuable insights into landowner decision-making and the impact of …

Refurbishing Used Gps Transmitters Improves Performance For Subsequent Deployments On Greater Sage-Grouse, Melissa S. Chelak, Michel T. Kohl, Justin R. Small, Kurt T. Smith, Aaron C. Pratt, Jeffrey L. Beck, Codi R. Backen, M. Brandon Flack, Hailey P. Wayment, Jason A. Wood, Ryan Howell, Trevon D. Strange, Lucian R. Mcdonald, Kezia R. Manlove, Shandra N. Frey, Randy T. Larsen, Brian A. Maxfield, David K. Dahlgren, Terry A. Messmer, David C. Stoner

Wildland Resources Student Research

Global Positioning Systems (GPS) radio transmitters are increasingly used across taxa to monitor animal populations. However, GPS transmitters can be susceptible to malfunctions that may result in location errors or data loss causing potential inferential bias that can have important implications for monitored species. Research using GPS transmitters on greater sage-grouse (Centrocercus urophasianus; sage-grouse) has increased, but few sage-grouse studies have evaluated GPS performance. Because sage-grouse management has been subject to intense legal and political scrutiny with consequential economic implications, reliable data acquisition is central to informed decision-making for the species. We evaluated differences in the performance of …

Halogeton And Greasewood Poisoning In Cattle And Sheep In Utah, E. Jane Kelly, Stephen T. Lee, Ammon Brown, Daniel Cook

Poisonous Plant Research (PPR)

Halogeton (Halogeton glomeratus) is a fast-growing annual plant while greasewood (Sarcobatus vermiculatus) is a perennial shrub of the Western States. Oxalates are the toxic principle in halogeton and greasewood. Most losses occur when hungry animals are allowed to graze in heavy stands of halogeton and greasewood. Halogeton and greasewood are always dangerous and become more toxic as the growing season progresses. Here we report on two clinical cases of halogeton and greasewood poisoning in cattle and sheep. Histologically, oxalate crystals were observed in the kidneys of the cow and sheep consistent with oxalate poisoning. Oxalate was …

Career: The Behavioral, Hormonal, And Neural Basis Of Coyote Monogamy, Sara M. Freeman

Funded Research Records

No abstract provided.

The Southwest Climate Adaptation Science Center (Sw Casc), Michelle Baker

Funded Research Records

No abstract provided.

Role Of Arbuscular Mycorrhizal Fungi In Maintaining Sustainable Agroecosystems, Anju Chaudhary, Shital Poudyal, Amita Kaundal

Plants, Soils, and Climate Faculty Publications

Arbuscular mycorrhizal (AM) fungi play a crucial role in maintaining sustainable agroecosystems by forming mutualistic relationships with plant roots, improving soil health, facilitating nutrient uptake, and enhancing resilience to abiotic stresses. The mutualistic relationship between AM fungi and plants promotes a balanced microbial community and improves soil structure by forming stable soil aggregates. Additionally, AM fungi can lower the adverse effects of high soil phosphorus (P) while also enhancing plant tolerance to drought, salinity, and heavy metal toxicity through osmotic regulation and antioxidant production. Arbuscular mycorrhizal fungi also support beneficial microorganisms, such as potassium (K)-solubilizing microbes and nitrogen (N)-transforming bacteria, …

"It's Definitely New And Different...It's Really Engaging": Understanding The Power Of Storytelling Towards Secure Password Creation, Rizu Paudel, Mahdi Nasrullah Al-Ameen

Computer Science Student Research

There is a dearth in existing literature to attain systematic understanding of leveraging digital storytelling in security designs. As we begin to address this gap, we focused on user authentication where the existing password composition policies and password meters often fail to help users around creating a strong and memorable password. To this end, we conducted a lab study with 19 participants, where we updated our initial designs in an iterative manner based on their feedback. We then conducted a between-subject online study with 104 participants over Amazon Mechanical Turk to evaluate our designs. We found that all of our …

Species Differences In The Biotransformation Of Aflatoxin B1: Primary Determinants Of Relative Carcinogenic Potency In Different Animal Species, David L. Eaton, David E. Williams, Roger A. Coulombe

Animal, Dairy, and Veterinary Science Faculty Publications

It has been known since the early days of the discovery of aflatoxin B1 (AFB1) that there were large species differences in susceptibility to AFB1. It was also evident early on that AFB1 itself was not toxic but required bioactivation to a reactive form. Over the past 60 years there have been thousands of studies to delineate the role of ~10 specific biotransformation pathways of AFB1, both phase I (oxidation, reduction) and phase II (hydrolysis, conjugation, secondary oxidations, and reductions of phase I metabolites). This review provides a historical context and substantive analysis of each of these pathways as contributors …

Extensive Admixture Among Karst-Obligate Salamanders Reveals Evidence Of Recent Divergence And Gene Exchange Through Aquifers, Chris C. Nice, Katherine L. Bell, Zachariah Gompert, Lauren K. Lucas, James R. Ott, Ruben U. Tovar, Paul Crump, Peter H. Diaz

Biology Faculty Publications

Karst ecosystems often contain extraordinary biodiversity, but the complex underground aquifers of karst regions present challenges for assessing and conserving stygobiont diversity and investigating their evolutionary history. We examined the karst-obligate salamanders of the Eurycea neotenes species complex in the Edwards Plateau region of central Texas using population genomics data to address questions about population connectivity and the potential for gene exchange within the underlying aquifer system. The E. neotenes species complex has historically been divided into three nominal species, but their status, and spatial extent of species ranges, have remained uncertain. We discovered evidence of extensive admixture among species …

Utah Producers And Soil Health: Statewide Survey Results, Peggy Petrzelka, Jessica Ulrich-Schad, Matt Yost, Jenae Dean, Earl Creech, Linda Schott, Tony Richards, Kristy Davis

All Current Publications

To gain soil health perspectives and actions from a representative sample of Utah farmers and ranchers, a mail and online survey of Utah producers was conducted in 2024, focused on those who indicated they produced crops in 2023. In this report, we provide an overview of the survey results, with a specific focus on producers’ views on soil health, indicators used for soil health, factors that influence soil health adoption, and information sources used for soil health.

Evaluating Elk Distribution And Conflict Under Proposed Management Alternatives At The National Elk Refuge In Jackson, Wyoming, Gavin G. Cotterill, Paul C. Cross, Eric K. Cole, Jonathan D. Cook, Margaret C. Mceachran, Tabitha A. Graves

Aspen Bibliography

We evaluated measurable attributes describing the current and future distribution of Cervus elaphus canadensis (elk) across a region surrounding Jackson, Wyoming, for five feedground management alternatives proposed by the U.S. Fish and Wildlife Service as a revision to 2007 "Bison and Elk Management Plan" of the National Elk Refuge. A resource selection function evaluated measurable attributes of interest to managers, including elk use of private property and sensitive habitat types at monthly timesteps and varying winter conditions. The study area boundaries were created through an expert elicitation process and consist of the Jackson Elk Herd Unit, Grand Teton National Park, …

Key Virulence Factors Responsible For Differences In Pathogenicity Between Clinically Proven Live-Attenuated Japanese Encephalitis Vaccine Sa14-14-2 And Its Pre-Attenuated Highly Virulent Parent Sa14, Byung-Hak Song, Sang-Im Yun, Joseph L. Goldhardt, Jiyoun Kim, Young-Min Lee

Animal, Dairy, and Veterinary Science Student Research

Japanese encephalitis virus (JEV), a neuroinvasive and neurovirulent orthoflavivirus, can be prevented in humans with the SA₁₄-14-2 vaccine, a live-attenuated version derived from the wild-type SA₁₄ strain. To determine the viral factors responsible for the differences in pathogenicity between SA₁₄ and SA₁₄-14-2, we initially established a reverse genetics system that includes a pair of full-length infectious cDNAs for both strains. Using this cDNA pair, we then systematically exchanged genomic regions between SA14 and SA₁₄-14-2 to generate 20 chimeric viruses and evaluated their replication capability in cell culture and their pathogenic potential in …

The Continuing Search For A Better Mouse Trap: Two Tests Of A Practical, Low-Cost Camera Trap For Detecting And Observing Small Mammals, Raymond D. Dueser, John H. Porter, Nancy D. Moncrief

Wildland Resources Faculty Publications

The advent of digital wildlife cameras has led to a dramatic increase in the use of camera traps for mammalian biodiversity surveys, ecological studies and occupancy analyses. For cryptic mammals such as mice and shrews, whose small sizes pose many challenges for unconstrained digital photography, use of camera traps remains relatively infrequent. Here we use a practical, low-cost small mammal camera platform (the “MouseCam”) that is easy and inexpensive to fabricate and deploy and requires little maintenance beyond camera service. We tested the MouseCam in two applications: a study of small mammal species composition on two transects across a barrier …

Increased Positive Tree Species Mixture Effects On The Abundance And Richness Of Collembola With Stand Development In Canadian Boreal Forests, Yakun Zhang, Sai Peng, Zilong Ma, Chen Chen, Bilei Gao, Xinli Chen, Han Y.H. Chen

Aspen Bibliography

It is well established that species mixtures could enhance ecosystem functioning in diverse ecosystem types, with these benefits increasing over time. However, the impact of tree mixtures on Collembola communities following stand development in natural forests remains unclear, despite the critical roles Collembola plays in litter decomposition and nutrient cycling. We investigated the effects of tree species mixtures on Collembola abundance, diversity, and community structure by sampling pure and mixed jack pine (Pinus banksiana Lamb.) and trembling aspen (Populus tremuloides Michx.) of 15-year-old and 41-year-old stands in natural boreal forest. In total, 6,620 individuals of Collembola were identified …

Selectivity Of Invasive Species Suppression Efforts Influences Control Efficacy, Rae Fadlovich, Kevin Landom, Timothy E. Walsworth

Watershed Sciences Student Research

1. Highly fecund invaders and size-selective suppression efforts often limit the effectiveness of invasive species control programs, as compensatory processes can allow suppressed populations to recover. While population models have long explored how demographic characteristics impact management feasibility, there is a growing need to evaluate how the selectivity of suppression efforts might impact the long-term feasibility of control.
2. We use a simulation framework that integrates age-based selectivity to evaluate the effect of increasing the range of ages selected for during harvest-based invasive species control. We applied this approach to common carp in Utah Lake, the location of one of the world's …